testing with python unittest testing with python unittest currently we are here: /home/emsley/autobuild/building/garib-pc-1.lmb.internal_2013-09-13__T03_40_01/coot-0.8-pre /home/emsley/autobuild/installed-pre-release-gtk2-python/bin/coot-real --no-graphics --script python-tests/coot_unittest.py INFO:: splash_screen_pixmap_dir /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/pixmaps INFO:: Colours file: /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/colours.def loaded INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif There are 1 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif Reading coordinate file: /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) DEBUG:: stating pydirectory /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/python INFO:: importing coot.py from /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/python/coot.py Importing python module coot using command from coot import * INFO:: coot.py imported INFO loading coot python modules Running python script /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/python/coot_load_modules.py Loading: coot_utils.py load redefine_functions.py Loading: filter.py Loading: coot_lsq.py Loading: shelx.py Loading: get_ebi.py Loading: local_code.py Loading: hello.py Good Morning None, Welcome to Coot. 0.8-pre (revision 4759) [with guile 1.8.8 embedded] [with python 2.7.5 embedded] (set-display-intro-string "Good Morning None, Welcome to Coot. 0.8-pre (revision 4759) [with guile 1.8.8 embedded] [with python 2.7.5 embedded]") Loading: mutate.py Loading: refmac.py Loading: libcheck.py Loading: gap.py Loading: fitting.py Loading: raster3d.py Loading: povray.py Loading: remote_control.py Loading: generic_objects.py Loading: ncs.py Loading: parse_pisa_xml.py Loading: cns2coot.py Loading: tips.py Loading: prodrg_import.py Loading: jligand.py Loading: americanisms.py Loading: group_settings.py Loading: brute_lsqman.py INFO:: loading preferences file /home/emsley/.coot-preferences/coot_preferences.py Running python script /home/emsley/.coot-preferences/coot_preferences.py (set-filter-fileselection-filenames 0) (unset-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 13.00) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/scheme (set-display-intro-string "Good morning Paul. Welcome to Coot") (set-display-lists-for-maps 0) INFO:: loading preferences file /home/emsley/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 0) (unset-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 13.00) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) INFO:: loading preferences file /home/emsley/.coot-preferences/mogul-interface.scm INFO:: loading preferences file /home/emsley/.coot-preferences/test-fit-step.scm (filter-fileselection-filenames-state) (get-active-map-drag-flag) Loading ~/.coot...done. Running python script python-tests/coot_unittest.py =============================================================== ==================== Testing ================================== =============================================================== WARNING:: unittest skip not avaliable!!!!!! ==== It seems CCP4_MASTER is setup === ==== CCP4_MASTER: /home/emsley/ccp4 test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... Molecule number -5 is not a valid model molecule ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... Error reading /home/emsley/data/greg-data/2WF6.pdb closing molecule number -1 ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: pre_n_molecules 1 post_n_molecules 1 ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... Reading coordinate file: /home/emsley/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/emsley/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 1 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:45:25_2013_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:45:25_2013_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:45:25_2013_modification_2.pdb.gz pre and post ins codes: A pass: ['A', 68, '', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'A', ' CA '] pass: ['A', 68, '', ' CA '] pass: ['A', 66, '', ' CA '] ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... WARNING:: Error reading bogus.map Read map bogus.map failed ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... WARNING:: Can't find file bogus.mtz valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.03 seconds to read MTZ file INFO:: 0.035 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.051 seconds for contour map INFO:: 0.152 seconds in total ok test07_1 (__main__.PdbMtzTestFunctions) Auto-read bad MTZ test ... WARNING:: file xx-missing.mtz does not exist got status: -1 >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/emsley/data/greg-data/broken.mtz INFO:: not an mtz file: /home/emsley/data/greg-data/broken.mtz got status: -1 ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... INFO:: map sigmas 0.311500996351 False ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... making conventional map from MTZ filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.033 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.049 seconds for contour map INFO:: 0.11 seconds in total ok test09_1 (__main__.PdbMtzTestFunctions) Sharpen map from map ... valid_labels(/home/emsley/data/greg-data/3hfl_sigmaa.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 96, 128, 132) INFO:: 0.021 seconds to read MTZ file INFO:: 0.019 seconds to initialize map INFO:: 0.029 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.83254e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.77531 Map minimum: ..... -1.05473 INFO:: 0.011 seconds for contour map INFO:: 0.083 seconds in total INFO:: map file type was determined to be CCP4 type allocating space in read_ccp4_map attempting to read CCP4 map: test-3hfl.map ========== file grid sampling: Nuvw = ( 96, 128, 132) closing CCP4 map: test-3hfl.map Map statistics: mean: 1.83254e-11 st.d: 0.260405 Map statistics: min: -1.05473, max: 1.77531 -0.983981 17 -0.842479 308 -0.700977 2677 -0.559475 12833 -0.417973 39023 -0.276471 86235 -0.134969 183659 0.00653285 251917 0.148035 122819 0.289537 40550 0.431039 26756 0.572541 19978 0.714043 13210 0.855545 6970 0.997047 2820 1.13855 873 1.28005 243 1.42155 85 1.56306 25 1.70456 10 1.84606 0 Map mean: ........ 1.83254e-11 Map rmsd: ........ 0.260405 Map maximum: ..... 1.77531 Map minimum: ..... -1.05473 ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 6 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 41 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 0 ALA N :: xyz = ( 49.89, 13.56, 4.156) A 0 ALA C :: xyz = ( 49.65, 11.73, 2.525) A 0 ALA CA :: xyz = ( 49.26, 12.27, 3.898) A 0 ALA O :: xyz = ( 49.63, 10.53, 2.245) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:45:26_2013_modification_0.pdb.gz Reading coordinate file: regression-test-terminal-residue.pdb PDB file regression-test-terminal-residue.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/91 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 7 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_regression-test-terminal-residue.pdb_Fri_Sep_13_04:45:26_2013_modification_0.pdb.gz ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 9 read successfully DEBUG:: there were 0 types with no dictionary DEUBG:: add_terminal_residue_using_phi_psi() 275 INFO:: backup file coot-backup/_home_emsley_data_greg-data_frag-2wot.pdb_Fri_Sep_13_04:45:26_2013_modification_0.pdb.gz adding whole residue triggered by atom 1/A/276 {ALA}/ N altLoc :: segid :: pos: (7.95956,25.0769,3.88408) B-factor: 30 with element N adding atom to existing residue 1/A/276 {ALA}/ C altLoc :: segid :: pos: (10.3577,25.1553,4.43381) B-factor: 30 (already has 1 atoms) adding atom to existing residue 1/A/276 {ALA}/ CA altLoc :: segid :: pos: (9.26201,24.4785,3.6171) B-factor: 30 (already has 2 atoms) adding atom to existing residue 1/A/276 {ALA}/ O altLoc :: segid :: pos: (10.6535,24.7432,5.55546) B-factor: 30 (already has 3 atoms) adding atom to existing residue 1/A/276 {ALA}/ CB altLoc :: segid :: pos: (9.55539,24.5518,2.12418) B-factor: 30 (already has 4 atoms) INFO:: 4 atoms added to molecule. INFO:: old n_atoms: 76 new: 81 DEUBG:: add_terminal_residue_using_phi_psi() 276 INFO:: backup file coot-backup/_home_emsley_data_greg-data_frag-2wot.pdb_Fri_Sep_13_04:45:26_2013_modification_1.pdb.gz adding whole residue triggered by atom 1/A/277 {ALA}/ N altLoc :: segid :: pos: (10.5277,26.4564,4.22323) B-factor: 30 with element N adding atom to existing residue 1/A/277 {ALA}/ C altLoc :: segid :: pos: (11.3064,27.175,6.44508) B-factor: 30 (already has 1 atoms) adding atom to existing residue 1/A/277 {ALA}/ CA altLoc :: segid :: pos: (11.5409,27.2225,4.93896) B-factor: 30 (already has 2 atoms) adding atom to existing residue 1/A/277 {ALA}/ O altLoc :: segid :: pos: (11.8153,26.2914,7.13472) B-factor: 30 (already has 3 atoms) adding atom to existing residue 1/A/277 {ALA}/ CB altLoc :: segid :: pos: (11.5498,28.6554,4.42226) B-factor: 30 (already has 4 atoms) INFO:: 4 atoms added to molecule. INFO:: old n_atoms: 81 new: 86 DEUBG:: add_terminal_residue_using_phi_psi() 276 WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... Symmetry available for this molecule Sphere mol: there are 4 residues in chain B Found 20 sphere atoms ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 11 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:26_2013_modification_0.pdb.gz residue info (should be False): False ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... Symmetry available for this molecule N /10/B is not found in this molecule: (12) atom selection from tutorial-modern.pdb INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:45:26_2013_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:45:26_2013_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:45:26_2013_modification_2.pdb.gz ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... Reading coordinate file: /home/emsley/data/greg-data/rotamer-test-fragment.pdb PDB file /home/emsley/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 13 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] ok test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... Reading coordinate file: /home/emsley/data/greg-data/res098.pdb PDB file /home/emsley/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 14 read successfully DEBUG:: there were 0 types with no dictionary For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 created 6 bond restraints created 6 angle restraints created 0 plane restraints created 1 chiral vol restraints created 13 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 15 and 15 of chain X Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 9.10451 Initial RMS Z values bonds: 0.404934 angles: 0.452855 torsions: N/A planes: 1.15167 non-bonded: 0 chiral vol: 0.162676 rama plot: N/A start_pos: N/A Minimum found (iteration number 186) at 6.27245 Final Estimated RMS Z Scores: bonds: 0.0592078 angles: 0.539637 torsions: N/A planes: 0.807452 non-bonded: 0 chiral vol: 0.376827 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 2.4 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_res098.pdb_Fri_Sep_13_04:45:27_2013_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 15 read successfully DEBUG:: there were 0 types with no dictionary valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.032 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.049 seconds for contour map INFO:: 0.109 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:28_2013_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:28_2013_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 12.0506 ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... Reading coordinate file: /home/emsley/data/greg-data/pdb3knw.ent PDB file /home/emsley/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links Symmetry available for this molecule INFO:: NCS chain comparison 185/199 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 17 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "EDO" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3knw.ent_Fri_Sep_13_04:45:28_2013_modification_0.pdb.gz se_1: [['SE ', ''], [0.7, 2.0, 'SE', ''], [58.8, 66.533, 0.047]] se_2: [['SE ', ''], [0.7, 2.0, 'SE', ''], [60.13112002923666, 69.34847968524429, -0.673518803101735]] ok test16_3 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 18 read successfully DEBUG:: there were 0 types with no dictionary valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.032 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.049 seconds for contour map INFO:: 0.109 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:28_2013_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... Reading coordinate file: /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 20 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-pepflip-test.pdb_Fri_Sep_13_04:45:29_2013_modification_0.pdb.gz flipped 65 A ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 21 read successfully DEBUG:: there were 0 types with no dictionary in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x5630c70 omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:45:29_2013_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:45:29_2013_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 flipped 11 A INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:45:29_2013_modification_2.pdb.gz created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 3397.26 Initial RMS Z values bonds: 15.4679 angles: 7.38705 torsions: N/A planes: 2.80521 non-bonded: 48.7437 chiral vol: 3.04463 rama plot: N/A start_pos: N/A Minimum found (iteration number 36) at -4817.07 Final Estimated RMS Z Scores: bonds: 2.38716 angles: 1.52188 torsions: N/A planes: 2.38488 non-bonded: 0.638809 chiral vol: 0.226738 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 4.005 Refinement elapsed time: 0.015 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:45:29_2013_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:45:29_2013_modification_4.pdb.gz ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:45:29_2013_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.73012 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -5997.66 Initial RMS Z values bonds: 1.78865 angles: 1.67802 torsions: N/A planes: 3.14799 non-bonded: 0.634811 chiral vol: 0.191647 rama plot: N/A start_pos: N/A Minimum found (iteration number 74) at -6102.11 Final Estimated RMS Z Scores: bonds: 2.1245 angles: 1.35379 torsions: N/A planes: 2.43993 non-bonded: 0.278486 chiral vol: 0.408672 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 4.141 Refinement elapsed time: 0.02 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:45:29_2013_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.032 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.051 seconds for contour map INFO:: 0.111 seconds in total created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 72 and 72 of chain B Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -2746.24 Initial RMS Z values bonds: 1.67379 angles: 1.06965 torsions: N/A planes: 0.911782 non-bonded: 9.24559 chiral vol: 1.46202 rama plot: N/A start_pos: N/A Minimum found (iteration number 13) at -2930.98 Final Estimated RMS Z Scores: bonds: 1.17098 angles: 1.38116 torsions: N/A planes: 1.07209 non-bonded: 1.06154 chiral vol: 0.446598 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 4.523 Refinement elapsed time: 0.007 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:30_2013_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. refined moved: d= 0.293387825752 ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 24 read successfully DEBUG:: there were 0 types with no dictionary here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:45:30_2013_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 imol: 24 residues: [['A', 93, ''], ['A', 92, ''], ['A', 3, ''], ['A', 5, '']] created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints Link restraints: 0 bond links 0 angle links 0 plane links Flanking residue restraints: 5 bond links 15 angle links 10 plane links initial distortion_score: -11033.5 Initial RMS Z values bonds: 1.8061 angles: 0.891239 torsions: N/A planes: 1.07498 non-bonded: 0 chiral vol: 0.668982 rama plot: N/A start_pos: N/A Minimum found (iteration number 21) at -11238.9 Final Estimated RMS Z Scores: bonds: 1.07027 angles: 0.63434 torsions: N/A planes: 0.854642 non-bonded: 0 chiral vol: 0.212347 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 5.083 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:45:30_2013_modification_1.pdb.gz INFO:: replace_coords: 23 atoms updated. imol: 24 residues: [['A', 41, ''], ['A', 42, ''], ['A', 40, ''], ['A', 39, ''], ['A', 43, '']] created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints created 84 restraints Link restraints: 4 bond links 12 angle links 8 plane links Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -13426.3 Initial RMS Z values bonds: 0.980695 angles: 1.01754 torsions: N/A planes: 3.84002 non-bonded: 0.677622 chiral vol: 10.2816 rama plot: N/A start_pos: N/A Minimum found (iteration number 69) at -16252.4 Final Estimated RMS Z Scores: bonds: 1.61925 angles: 1.63668 torsions: N/A planes: 1.89069 non-bonded: 0.00148089 chiral vol: 2.2007 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 5.494 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:45:30_2013_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. ======= got bond length 1.29549140818 ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 25 read successfully DEBUG:: there were 0 types with no dictionary valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.033 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.049 seconds for contour map INFO:: 0.11 seconds in total created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -9612.98 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 4.28599 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A Minimum found (iteration number 54) at -11863.7 Final Estimated RMS Z Scores: bonds: 1.68281 angles: 1.81047 torsions: N/A planes: 2.09142 non-bonded: 0.00336553 chiral vol: 2.42505 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 6.004 Refinement elapsed time: 0.088 refinement results: ['', 0, [['Bonds', 'Bonds: 1.683', 1.6828066110610962], ['Angles', 'Angles: 1.810', 1.8104748725891113], ['Planes', 'Planes: 2.091', 2.0914218425750732], ['Non-bonded', 'Non-bonded: 0.058', 0.05801321938633919], ['Chirals', 'Chirals: 2.425', 2.4250476360321045]]] ow factor 2.00243774056 INFO:: setting refinement weight to 14.9635006371 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1426.62 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 4.28599 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A Minimum found (iteration number 10) at -2820.69 Final Estimated RMS Z Scores: bonds: 0.476411 angles: 1.30327 torsions: N/A planes: 1.97227 non-bonded: 0.00079874 chiral vol: 1.28202 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 6.16 Refinement elapsed time: 0.155 refinement results: ['', 0, [['Bonds', 'Bonds: 0.476', 0.4764111638069153], ['Angles', 'Angles: 1.303', 1.3032727241516113], ['Planes', 'Planes: 1.972', 1.9722687005996704], ['Non-bonded', 'Non-bonded: 0.028', 0.028261985629796982], ['Chirals', 'Chirals: 1.282', 1.2820171117782593]]] ow factor 1.25849242508 INFO:: setting refinement weight to 9.44782857351 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -424.029 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 4.28599 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A Minimum found (iteration number 2) at -1731.74 Final Estimated RMS Z Scores: bonds: 0.349261 angles: 1.23969 torsions: N/A planes: 1.95913 non-bonded: 0.000572745 chiral vol: 1.1417 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 6.312 Refinement elapsed time: 0.151 refinement results: ['', 0, [['Bonds', 'Bonds: 0.349', 0.34926125407218933], ['Angles', 'Angles: 1.240', 1.2396926879882812], ['Planes', 'Planes: 1.959', 1.9591293334960938], ['Non-bonded', 'Non-bonded: 0.024', 0.02393209934234619], ['Chirals', 'Chirals: 1.142', 1.1417003870010376]]] ow factor 1.17244591564 INFO:: setting refinement weight to 6.87300018488 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 44.0016 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 4.28599 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A Minimum found (iteration number 63) at -1225.73 Final Estimated RMS Z Scores: bonds: 0.298593 angles: 1.21292 torsions: N/A planes: 1.94519 non-bonded: 0.000517479 chiral vol: 1.08218 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 6.505 Refinement elapsed time: 0.193 refinement results: ['', 0, [['Bonds', 'Bonds: 0.299', 0.29859334230422974], ['Angles', 'Angles: 1.213', 1.2129229307174683], ['Planes', 'Planes: 1.945', 1.9451936483383179], ['Non-bonded', 'Non-bonded: 0.023', 0.022748155519366264], ['Chirals', 'Chirals: 1.082', 1.0821791887283325]]] ow factor 1.13472227752 INFO:: setting refinement weight to 5.33786014132 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 323.047 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 4.28599 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A Minimum found (iteration number 2) at -924.971 Final Estimated RMS Z Scores: bonds: 0.272194 angles: 1.19712 torsions: N/A planes: 1.93037 non-bonded: 0.00050089 chiral vol: 1.04579 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 6.761 Refinement elapsed time: 0.257 refinement results: ['', 0, [['Bonds', 'Bonds: 0.272', 0.27219441533088684], ['Angles', 'Angles: 1.197', 1.197117567062378], ['Planes', 'Planes: 1.930', 1.9303730726242065], ['Non-bonded', 'Non-bonded: 0.022', 0.022380568087100983], ['Chirals', 'Chirals: 1.046', 1.045788049697876]]] ow factor 1.11136827618 INFO:: setting refinement weight to 4.32166596877 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 507.762 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 4.28599 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A Minimum found (iteration number 27) at -726.414 Final Estimated RMS Z Scores: bonds: 0.256858 angles: 1.18565 torsions: N/A planes: 1.91639 non-bonded: 0.000498455 chiral vol: 1.02023 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 7.004 Refinement elapsed time: 0.242 refinement results: ['', 0, [['Bonds', 'Bonds: 0.257', 0.2568584382534027], ['Angles', 'Angles: 1.186', 1.1856460571289062], ['Planes', 'Planes: 1.916', 1.9163944721221924], ['Non-bonded', 'Non-bonded: 0.022', 0.02232610248029232], ['Chirals', 'Chirals: 1.020', 1.020233392715454]]] ow factor 1.09478309005 ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... Reading coordinate file: /home/emsley/data/greg-data/alt-conf-waters.pdb PDB file /home/emsley/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 27 read successfully DEBUG:: there were 0 types with no dictionary masking....masking done INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-waters.pdb_Fri_Sep_13_04:45:32_2013_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... Reading coordinate file: /home/emsley/data/greg-data/backrub-fragment.pdb PDB file /home/emsley/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 28 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Fri_Sep_13_04:45:33_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Fri_Sep_13_04:45:33_2013_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,/RNASE3GMP/COMPLEX/FWT,/RNASE3GMP/COMPLEX/PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.033 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.047 seconds for contour map INFO:: 0.107 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... Reading coordinate file: /home/emsley/data/greg-data/test-TER-OXT.pdb PDB file /home/emsley/data/greg-data/test-TER-OXT.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 31 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_test-TER-OXT.pdb_Fri_Sep_13_04:45:33_2013_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45 WARNING:: This residue already has an OXT - aborting found TER TER 25 ASP A 14 ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... Reading coordinate file: /home/emsley/data/greg-data/val.pdb PDB file /home/emsley/data/greg-data/val.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 32 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_home_emsley_data_greg-data_val.pdb_Fri_Sep_13_04:45:33_2013_modification_0.pdb.gz ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... Reading coordinate file: /home/emsley/data/greg-data/2yie-frag.pdb PDB file /home/emsley/data/greg-data/2yie-frag.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 33 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_2yie-frag.pdb_Fri_Sep_13_04:45:34_2013_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0404315 rms devi: 0.0471732 max devi: 0.0832785 min devi: 0.0130055 ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 34 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NCO" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NCO.cif INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Fri_Sep_13_04:45:34_2013_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0434566 rms devi: 0.0477873 max devi: 0.073989 min devi: 0.0147744 ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 35 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Fri_Sep_13_04:45:34_2013_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0394451 rms devi: 0.0444615 max devi: 0.0694865 min devi: 0.0151341 ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... failed to delete residue atoms A 88 :A: ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.033 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.041 seconds for contour map INFO:: 0.102 seconds in total valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.024 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.04 seconds for contour map INFO:: 0.101 seconds in total Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 38 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.00140896 st.d: 0.305562 Map statistics: min: -0.921659, max: 3.05176 -0.822323 82 -0.623652 4584 -0.424981 63986 -0.22631 186046 -0.0276392 273649 0.171032 117231 0.369703 35042 0.568374 22373 0.767045 16065 0.965716 9789 1.16439 5062 1.36306 2263 1.56173 811 1.7604 219 1.95907 53 2.15774 10 2.35641 9 2.55508 3 2.75376 2 2.95243 1 3.1511 0 high-values: [0.8227398991584778, 1.0119965076446533, 1.0171315670013428, 1.0682491064071655, 0.7381036281585693, 0.8017536401748657, 0.6875786781311035, 0.6362036466598511, 1.0157028436660767, 0.9525023698806763, 0.9898293018341064] low values: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] Map statistics: mean: -0.00140896 st.d: 0.0605043 Map statistics: min: -2.99276, max: 0.774316 -2.89858 4 -2.71023 3 -2.52188 6 -2.33352 5 -2.14517 7 -1.95681 8 -1.76846 18 -1.58011 41 -1.39175 76 -1.2034 172 -1.01505 335 -0.826691 597 -0.638337 793 -0.449984 1105 -0.26163 1562 -0.0732758 724217 0.115078 4310 0.303432 3125 0.491786 838 0.68014 58 0.868493 0 diff-high-values: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] diff-low-values: [-0.5536488890647888, -0.9707267880439758, -0.6932031512260437, -0.8488963842391968, -0.8271133303642273, -1.0860068798065186, -1.2907465696334839, -1.183866262435913, -0.9473038911819458, -0.893179178237915] ok test29_1 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.025 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.033 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.041 seconds for contour map INFO:: 0.102 seconds in total valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.025 seconds to read MTZ file INFO:: 0.048 seconds to initialize map INFO:: 0.045 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.16132e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.055 seconds for contour map INFO:: 0.176 seconds in total Map statistics: mean: -3.34695e-06 st.d: 0.311048 Map statistics: min: -0.916532, max: 3.05151 -0.817331 86 -0.618929 5071 -0.420526 68107 -0.222124 192102 -0.0237222 261140 0.17468 116277 0.373082 35835 0.571484 23249 0.769886 16639 0.968288 10089 1.16669 5201 1.36509 2311 1.56349 835 1.7619 228 1.9603 60 2.1587 18 2.3571 14 2.55551 9 2.75391 6 2.95231 3 3.15071 0 Map statistics: mean: 3.34818e-06 st.d: 0.00108591 Map statistics: min: -0.0109202, max: 0.00950789 -0.0104095 5 -0.00938806 12 -0.00836666 25 -0.00734526 37 -0.00632385 61 -0.00530245 326 -0.00428105 1710 -0.00325964 6306 -0.00223824 24803 -0.00121684 106344 -0.000195435 362832 0.000825968 177538 0.00184737 36579 0.00286877 12395 0.00389018 5092 0.00491158 2108 0.00593298 781 0.00695439 243 0.00797579 65 0.00899719 18 0.0100186 0 INFO:: map sigmas: normal 0.311048001051 and diff-map: 0.00108590547461 ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... Reading coordinate file: /home/emsley/data/greg-data/multi-carbo-coot-2.pdb PDB file /home/emsley/data/greg-data/multi-carbo-coot-2.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 45 read successfully DEBUG:: there were 2 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "FUC" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/f/FUC.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAG.cif bond-length: 2.97694071154 created 46 bond restraints created 82 angle restraints created 2 plane restraints created 8 chiral vol restraints created 138 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A INFO:: glycosidic_linkage type :ALPHA1-4: Link restraints: 1 bond links 3 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 7100.08 Initial RMS Z values bonds: 11.3589 angles: 3.25886 torsions: N/A planes: 0.0835273 non-bonded: 0.0943839 chiral vol: 0.903463 rama plot: N/A start_pos: N/A Minimum found (iteration number 894) at 0.755133 Final Estimated RMS Z Scores: bonds: 0.0228192 angles: 0.0911278 torsions: N/A planes: 0.00142033 non-bonded: 5.56479e-06 chiral vol: 0.0465342 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 12.102 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_multi-carbo-coot-2.pdb_Fri_Sep_13_04:45:37_2013_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. bond-length: 1.44039341976 ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... Reading coordinate file: /home/emsley/data/greg-data/monomer-VAL.pdb PDB file /home/emsley/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 46 read successfully DEBUG:: there were 0 types with no dictionary created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 4.99701 Initial RMS Z values bonds: 0.542493 angles: 0.164062 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.451586 rama plot: N/A start_pos: N/A Minimum found (iteration number 80) at 0.247633 Final Estimated RMS Z Scores: bonds: 0.0110165 angles: 0.0948618 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.144792 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 12.735 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:45:38_2013_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 46 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:45:38_2013_modification_1.pdb.gz restoring from backup 2 2 Reading coordinate file: coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:45:38_2013_modification_0.pdb.gz PDB file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:45:38_2013_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 4.99701 Initial RMS Z values bonds: 0.542493 angles: 0.164062 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.451586 rama plot: N/A start_pos: N/A Minimum found (iteration number 80) at 0.247633 Final Estimated RMS Z Scores: bonds: 0.0110165 angles: 0.0948618 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.144792 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 12.818 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:45:38_2013_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. ok test32_0 (__main__.PdbMtzTestFunctions) Test for mangling of hydrogen names from a PDB v 3.0 ... Reading coordinate file: /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 47 read successfully DEBUG:: there were 0 types with no dictionary created 17 bond restraints created 31 angle restraints created 0 plane restraints created 1 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 6 and 6 of chain B Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 1370.91 Initial RMS Z values bonds: 5.62114 angles: 3.43297 torsions: N/A planes: N/A non-bonded: 3.49142 chiral vol: 0.753357 rama plot: N/A start_pos: N/A Minimum found (iteration number 282) at 0.473499 Final Estimated RMS Z Scores: bonds: 0.0098544 angles: 0.120821 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.139004 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 13.652 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Fri_Sep_13_04:45:39_2013_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... looping over restraint Symmetry available for this molecule created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 28 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 8784.3 Initial RMS Z values bonds: 1.1515 angles: 0.847578 torsions: N/A planes: 3.05577 non-bonded: 116.199 chiral vol: 0.757848 rama plot: N/A start_pos: N/A Minimum found (iteration number 5) at -272.29 Final Estimated RMS Z Scores: bonds: 0.260441 angles: 0.231898 torsions: N/A planes: 0.210156 non-bonded: 0.00234077 chiral vol: 0.0806096 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 13.704 Refinement elapsed time: 0.028 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:45:39_2013_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. Bond-length: 2.84995723167 pass intermediate 2.8 tolerance test looping over restraint created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 3426.14 Initial RMS Z values bonds: 17.5579 angles: 0.231898 torsions: N/A planes: 0.210156 non-bonded: 0 chiral vol: 0.0806096 rama plot: N/A start_pos: N/A Minimum found (iteration number 4) at -313.089 Final Estimated RMS Z Scores: bonds: 0.0785105 angles: 0.0989261 torsions: N/A planes: 0.262906 non-bonded: 0 chiral vol: 0.0197618 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 13.738 Refinement elapsed time: 0.019 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:45:39_2013_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. OK plane atom CB Bond-length: 1.51391136182 ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... -- new structure created SUMMARY:: rc CIFRC_Ok or newly created. ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 49 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "ACT" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ACT.cif There are 2 data in /home/emsley/data/greg-data/libcheck_ACT.cif Welcome to Coot looping over restraint created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 15 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 10588.6 Initial RMS Z values bonds: 0.0119892 angles: 0.00653967 torsions: N/A planes: 0 non-bonded: 755.759 chiral vol: N/A rama plot: N/A start_pos: N/A Minimum found (iteration number 63) at -79.5264 Final Estimated RMS Z Scores: bonds: 0.0182658 angles: 0.103211 torsions: N/A planes: 0.0267938 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 14.515 Refinement elapsed time: 0.053 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-ACT.pdb_Fri_Sep_13_04:45:40_2013_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 50 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_2.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_3.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_6.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:40_2013_modification_7.pdb.gz ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... Symmetry available for this molecule Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:45:41_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:41_2013_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. distances: [20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966] ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... found 6 neighbours [['A', 39, ''], ['A', 41, ''], ['A', 38, ''], ['B', 61, ''], ['A', 42, ''], ['B', 60, '']] found 0 neighbours [] ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 53 read successfully DEBUG:: there were 0 types with no dictionary ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... in new_molecule_by_residue_type_selection Something bad happened - No residues selected in new_molecule_by_residue_type_selection Something bad happened - No residues selected ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:41_2013_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 54 read successfully DEBUG:: there were 0 types with no dictionary Rotamer 0 : m-85 100.0 Rotamer 1 : t80 90.1668395996 Rotamer 2 : p90 50.7077865601 Rotamer 3 : m -30 21.4231548309 Rotamer 4 : m -30 21.4231548309 ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... Reading coordinate file: /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 50/87 Molecule 55 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 55chain: A ------------------------------------------------- chain A ------------------------------------------------- INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID > target seq: DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 163.5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Fri_Sep_13_04:45:43_2013_modification_0.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 The alignment resulted in the following Insertions (coalesced): from 1 to 4 ASP VAL SER from 11 to 14 LEU PRO PRO from 62 to 64 PRO GLY Insertions (singles): [spec: 4 "A" 1 ""] -> ASP [spec: 4 "A" 2 ""] -> VAL [spec: 4 "A" 3 ""] -> SER [spec: 4 "A" 11 ""] -> LEU [spec: 4 "A" 12 ""] -> PRO [spec: 4 "A" 13 ""] -> PRO [spec: 4 "A" 62 ""] -> PRO [spec: 4 "A" 63 ""] -> GLY Deletions: [spec: 4 "A" 24 ""] [spec: 4 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions ::::: [55, 'A', 1, ''] False False ::::: [55, 'A', 4, ''] True True ::::: [55, 'A', 59, ''] True True ::::: [55, 'A', 60, ''] False False ::::: [55, 'A', 61, ''] False False ::::: [55, 'A', 93, ''] True True ::::: [55, 'A', 94, ''] False False ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 56 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:43_2013_modification_0.pdb.gz Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 57 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:44_2013_modification_0.pdb.gz ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... Reading coordinate file: /home/emsley/data/greg-data/pdb3hfl.ent PDB file /home/emsley/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 58 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "PCA" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PCA.cif valid_labels(/home/emsley/data/greg-data/3hfl_sigmaa.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.018 seconds to read MTZ file INFO:: 0.007 seconds to initialize map INFO:: 0.012 seconds for FFT INFO:: 0.001 seconds for statistics Map mean: ........ 2.00384e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.009 seconds for contour map INFO:: 0.047 seconds in total INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Fri_Sep_13_04:45:45_2013_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.83361 INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Fri_Sep_13_04:45:45_2013_modification_1.pdb.gz ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:45:45_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:45:45_2013_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269035 rms devi: 0.337196 max devi: 0.547544 min devi: 0.0817551 mutated base to type C - was A INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:45:45_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:45:45_2013_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269035 rms devi: 0.337196 max devi: 0.547544 min devi: 0.0817551 mutated base to type Cr - was A ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0.00589883 rms devi: 0.00670957 max devi: 0.0101325 min devi: 0.00258111 INFO:: 5 matched atoms had: mean devi: 0.00725623 rms devi: 0.00778801 max devi: 0.0125644 min devi: 0.00456024 INFO:: 5 matched atoms had: mean devi: 0.271793 rms devi: 0.336384 max devi: 0.533839 min devi: 0.0878288 INFO:: 5 matched atoms had: mean devi: 0.26776 rms devi: 0.326512 max devi: 0.505569 min devi: 0.10459 INFO:: 5 matched atoms had: mean devi: 0.271823 rms devi: 0.336416 max devi: 0.53388 min devi: 0.0879009 INFO:: 5 matched atoms had: mean devi: 0.267791 rms devi: 0.326544 max devi: 0.505617 min devi: 0.104522 INFO:: 5 matched atoms had: mean devi: 0.00717866 rms devi: 0.00770023 max devi: 0.0124098 min devi: 0.00457508 INFO:: 5 matched atoms had: mean devi: 0.00574436 rms devi: 0.00657052 max devi: 0.0099594 min devi: 0.0024248 INFO:: 5 matched atoms had: mean devi: 0.271762 rms devi: 0.336353 max devi: 0.533797 min devi: 0.0877567 INFO:: 5 matched atoms had: mean devi: 0.267729 rms devi: 0.326479 max devi: 0.505521 min devi: 0.104657 INFO:: 5 matched atoms had: mean devi: 0.00585391 rms devi: 0.00666923 max devi: 0.0100827 min devi: 0.00253528 INFO:: 5 matched atoms had: mean devi: 0.00722485 rms devi: 0.00775255 max devi: 0.0125025 min devi: 0.00456535 INFO:: 5 matched atoms had: mean devi: 0.00580961 rms devi: 0.00662938 max devi: 0.0100332 min devi: 0.00249036 INFO:: 5 matched atoms had: mean devi: 0.00719394 rms devi: 0.00771755 max devi: 0.0124407 min devi: 0.00457156 INFO:: 5 matched atoms had: mean devi: 0.267807 rms devi: 0.326561 max devi: 0.505641 min devi: 0.104488 INFO:: 5 matched atoms had: mean devi: 0.27187 rms devi: 0.336463 max devi: 0.533942 min devi: 0.088009 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270191 rms devi: 0.336363 max devi: 0.538427 min devi: 0.0854029 mutated base to type DC INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.271895 rms devi: 0.336278 max devi: 0.534478 min devi: 0.0923473 mutated base to type DG INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043292 rms devi: 0.00481764 max devi: 0.00738267 min devi: 0.00186162 mutated base to type DA INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.265718 rms devi: 0.326008 max devi: 0.501859 min devi: 0.0926641 mutated base to type DT INFO:: 5 matched atoms had: mean devi: 0.00589883 rms devi: 0.00670957 max devi: 0.0101325 min devi: 0.00258111 INFO:: 5 matched atoms had: mean devi: 0.00725623 rms devi: 0.00778801 max devi: 0.0125644 min devi: 0.00456024 INFO:: 5 matched atoms had: mean devi: 0.271793 rms devi: 0.336384 max devi: 0.533839 min devi: 0.0878288 INFO:: 5 matched atoms had: mean devi: 0.26776 rms devi: 0.326512 max devi: 0.505569 min devi: 0.10459 INFO:: 5 matched atoms had: mean devi: 0.271823 rms devi: 0.336416 max devi: 0.53388 min devi: 0.0879009 INFO:: 5 matched atoms had: mean devi: 0.267791 rms devi: 0.326544 max devi: 0.505617 min devi: 0.104522 INFO:: 5 matched atoms had: mean devi: 0.00717866 rms devi: 0.00770023 max devi: 0.0124098 min devi: 0.00457508 INFO:: 5 matched atoms had: mean devi: 0.00574436 rms devi: 0.00657052 max devi: 0.0099594 min devi: 0.0024248 INFO:: 5 matched atoms had: mean devi: 0.271762 rms devi: 0.336353 max devi: 0.533797 min devi: 0.0877567 INFO:: 5 matched atoms had: mean devi: 0.267729 rms devi: 0.326479 max devi: 0.505521 min devi: 0.104657 INFO:: 5 matched atoms had: mean devi: 0.00585391 rms devi: 0.00666923 max devi: 0.0100827 min devi: 0.00253528 INFO:: 5 matched atoms had: mean devi: 0.00722485 rms devi: 0.00775255 max devi: 0.0125025 min devi: 0.00456535 INFO:: 5 matched atoms had: mean devi: 0.00580961 rms devi: 0.00662938 max devi: 0.0100332 min devi: 0.00249036 INFO:: 5 matched atoms had: mean devi: 0.00719394 rms devi: 0.00771755 max devi: 0.0124407 min devi: 0.00457156 INFO:: 5 matched atoms had: mean devi: 0.267807 rms devi: 0.326561 max devi: 0.505641 min devi: 0.104488 INFO:: 5 matched atoms had: mean devi: 0.27187 rms devi: 0.336463 max devi: 0.533942 min devi: 0.088009 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270191 rms devi: 0.336363 max devi: 0.538427 min devi: 0.0854029 mutated base to type Cd INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.271895 rms devi: 0.336278 max devi: 0.534478 min devi: 0.0923473 mutated base to type Gd INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043292 rms devi: 0.00481764 max devi: 0.00738267 min devi: 0.00186162 mutated base to type Ad INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:45:45_2013_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.265718 rms devi: 0.326008 max devi: 0.501859 min devi: 0.0926641 mutated base to type Td ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... Symmetry available for this molecule INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:45_2013_modification_0.pdb.gz ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... Reading coordinate file: /home/emsley/data/greg-data/some-waters-with-ter.pdb PDB file /home/emsley/data/greg-data/some-waters-with-ter.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 65 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_some-waters-with-ter.pdb_Fri_Sep_13_04:45:46_2013_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... Reading coordinate file: /home/emsley/data/greg-data/tm+some-waters.pdb PDB file /home/emsley/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 66 read successfully DEBUG:: there were 0 types with no dictionary Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 0.2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.311501 INFO:: Using density cut-off: 0.0623002 (0.2 sigma) (mean -0.0338214 stdev: 0.146177) INFO:: Using water to protein distance limits: 1.5 3.6 Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 28.11, 32.19, 9.322) is too big to be water INFO:: cluster at xyz = ( 70.02, 19.14, 18.63) is too big to be water INFO:: cluster at xyz = ( 52.69, 10.8, 11.54) is too big to be water INFO:: cluster at xyz = ( 73.3, 12.31, 14.45) is too big to be water INFO:: cluster at xyz = ( 39.77, 8.163, 19.52) is too big to be water INFO:: cluster at xyz = ( 53.3, -4.948, -2.745) is too big to be water INFO:: cluster at xyz = ( 40.96, 7.032, 16.25) is too big to be water INFO:: found 68 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tm+some-waters.pdb_Fri_Sep_13_04:45:47_2013_modification_0.pdb.gz INFO:: Adding to solvent chain: D ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 67 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:48_2013_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... Reading coordinate file: /home/emsley/data/greg-data/water-test-no-cell.pdb PDB file /home/emsley/data/greg-data/water-test-no-cell.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 68 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_water-test-no-cell.pdb_Fri_Sep_13_04:45:52_2013_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules Reading coordinate file: /home/emsley/data/greg-data/pathological-water-test.pdb PDB file /home/emsley/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 69 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_pathological-water-test.pdb_Fri_Sep_13_04:45:53_2013_modification_0.pdb.gz INFO:: moved 181 water molecules ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... Symmetry available for this molecule valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.025 seconds to read MTZ file INFO:: 0.011 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.001 seconds for statistics Map mean: ........ 1.06932e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.02 seconds for contour map INFO:: 0.073 seconds in total INFO:: Masking around 58 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 94 ALA N :: xyz = ( 58.52, 2.828, -1.801) A 94 ALA C :: xyz = ( 59.88, 1.672, -3.498) A 94 ALA CA :: xyz = ( 59.8, 2.182, -2.063) A 94 ALA O :: xyz = ( 58.86, 1.305, -4.092) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:53_2013_modification_0.pdb.gz ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... Symmetry available for this molecule WARNING:: failed to find master_chain_id "A" in 0 NCS ghosts ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 73 read successfully DEBUG:: there were 0 types with no dictionary 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 74 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "TAR" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TAR.cif Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 75 read successfully DEBUG:: there were 0 types with no dictionary Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 76 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NPO" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NPO.cif -------- starting chain list ----------- ['A', 'B', 'C', 'D', ''] -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0 0 0.333333 pre-trans: 0 0 0 Symmetry available for this molecule ['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K'] ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... Symmetry available for this molecule Symmetry available for this molecule INFO:: Matching/moving molecule number 79 to 78 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.0353197 rms devi: 0.0377881 max devi: 0.0545286 min devi: 0.016676 INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076) INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:56_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 80 read successfully DEBUG:: there were 0 types with no dictionary Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 81 read successfully DEBUG:: there were 0 types with no dictionary INFO:: spacegroup: P 21 21 21 INFO:: spacegroup: C 1 2 1 INFO:: Matching/moving molecule number 80 to 81 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.502333 rms devi: 0.593803 max devi: 1.67852 min devi: 0.0431788 INFO:: Axis orientation: ( 0.567, -0.7175, 0.4046) INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019) INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:57_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 82 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:58_2013_modification_0.pdb.gz 0 [82, 'A', 1, ''] 1 [82, 'A', 2, ''] 2 [82, 'A', 3, ''] 3 [82, 'A', 4, ''] 4 [82, 'A', 5, ''] 5 [82, 'A', 6, ''] 6 [82, 'A', 7, ''] 7 [82, 'A', 8, ''] 8 [82, 'A', 9, ''] 9 [82, 'A', 10, ''] 10 [82, 'A', 11, ''] 11 [82, 'A', 12, ''] 12 [82, 'A', 13, ''] 13 [82, 'A', 14, ''] 14 [82, 'A', 15, ''] 15 [82, 'A', 16, ''] 16 [82, 'A', 17, ''] 17 [82, 'A', 18, ''] 18 [82, 'A', 19, ''] 19 [82, 'A', 20, ''] 20 [82, 'A', 21, ''] 21 [82, 'A', 22, ''] 22 [82, 'A', 23, ''] 23 [82, 'A', 24, ''] 24 [82, 'A', 25, ''] 25 [82, 'A', 26, ''] 26 [82, 'A', 27, ''] 27 [82, 'A', 28, ''] 28 [82, 'A', 29, ''] 29 [82, 'A', 30, ''] 30 [82, 'A', 31, ''] 31 [82, 'A', 32, ''] 32 [82, 'A', 33, ''] 33 [82, 'A', 34, ''] 34 [82, 'A', 35, ''] 35 [82, 'A', 36, ''] 36 [82, 'A', 37, ''] 36 [82, 'A', 37, ''] 37 [82, 'A', 38, ''] 38 [82, 'A', 39, ''] 39 [82, 'A', 40, ''] 40 [82, 'A', 41, ''] 41 [82, 'A', 42, ''] 42 [82, 'A', 43, ''] 43 [82, 'A', 44, ''] 44 [82, 'A', 45, ''] 45 [82, 'A', 46, ''] 46 [82, 'A', 47, ''] 47 [82, 'A', 48, ''] 48 [82, 'A', 49, ''] 49 [82, 'A', 50, ''] 50 [82, 'A', 51, ''] 51 [82, 'A', 52, ''] 52 [82, 'A', 53, ''] 53 [82, 'A', 54, ''] 54 [82, 'A', 55, ''] 55 [82, 'A', 56, ''] 56 [82, 'A', 57, ''] 57 [82, 'A', 58, ''] 58 [82, 'A', 59, ''] 59 [82, 'A', 60, ''] 60 [82, 'A', 61, ''] 61 [82, 'A', 62, ''] 62 [82, 'A', 63, ''] 63 [82, 'A', 64, ''] 64 [82, 'A', 65, ''] 65 [82, 'A', 66, ''] 66 [82, 'A', 67, ''] 67 [82, 'A', 68, ''] 68 [82, 'A', 69, ''] 69 [82, 'A', 70, ''] 70 [82, 'A', 71, ''] 71 [82, 'A', 72, ''] 72 [82, 'A', 73, ''] 73 [82, 'A', 74, ''] 74 [82, 'A', 75, ''] 75 [82, 'A', 76, ''] 76 [82, 'A', 77, ''] 77 [82, 'A', 78, ''] 78 [82, 'A', 79, ''] 79 [82, 'A', 80, ''] 80 [82, 'A', 81, ''] 81 [82, 'A', 82, ''] 82 [82, 'A', 83, ''] 83 [82, 'A', 84, ''] 84 [82, 'A', 85, ''] 85 [82, 'A', 86, ''] 86 [82, 'A', 87, ''] 87 [82, 'A', 88, ''] 88 [82, 'A', 89, ''] 89 [82, 'A', 90, ''] 90 [82, 'A', 91, ''] 91 [82, 'A', 92, ''] 92 [82, 'A', 93, ''] 93 [82, 'B', 1, ''] 94 [82, 'B', 2, ''] 95 [82, 'B', 3, ''] 96 [82, 'B', 4, ''] 97 [82, 'B', 5, ''] 98 [82, 'B', 6, ''] 99 [82, 'B', 7, ''] 100 [82, 'B', 8, ''] 101 [82, 'B', 9, ''] 102 [82, 'B', 10, ''] 103 [82, 'B', 11, ''] 104 [82, 'B', 12, ''] 105 [82, 'B', 13, ''] 106 [82, 'B', 14, ''] 107 [82, 'B', 15, ''] 108 [82, 'B', 16, ''] 109 [82, 'B', 17, ''] 110 [82, 'B', 18, ''] 111 [82, 'B', 19, ''] 112 [82, 'B', 20, ''] 113 [82, 'B', 21, ''] 114 [82, 'B', 22, ''] 115 [82, 'B', 23, ''] 116 [82, 'B', 24, ''] 117 [82, 'B', 25, ''] 118 [82, 'B', 26, ''] 119 [82, 'B', 27, ''] 120 [82, 'B', 28, ''] 121 [82, 'B', 29, ''] 122 [82, 'B', 30, ''] 123 [82, 'B', 31, ''] 124 [82, 'B', 32, ''] 125 [82, 'B', 33, ''] 126 [82, 'B', 34, ''] 127 [82, 'B', 35, ''] 128 [82, 'B', 36, ''] 129 [82, 'B', 37, ''] 130 [82, 'B', 38, ''] 131 [82, 'B', 39, ''] 132 [82, 'B', 40, ''] 133 [82, 'B', 41, ''] 134 [82, 'B', 42, ''] 135 [82, 'B', 43, ''] 136 [82, 'B', 44, ''] 137 [82, 'B', 45, ''] 138 [82, 'B', 46, ''] 139 [82, 'B', 47, ''] 140 [82, 'B', 48, ''] 141 [82, 'B', 49, ''] 142 [82, 'B', 50, ''] 143 [82, 'B', 51, ''] 144 [82, 'B', 52, ''] 145 [82, 'B', 53, ''] 146 [82, 'B', 54, ''] 147 [82, 'B', 55, ''] 148 [82, 'B', 56, ''] 149 [82, 'B', 57, ''] 150 [82, 'B', 58, ''] 151 [82, 'B', 59, ''] 152 [82, 'B', 60, ''] 153 [82, 'B', 61, ''] 154 [82, 'B', 62, ''] 155 [82, 'B', 63, ''] 156 [82, 'B', 64, ''] 157 [82, 'B', 65, ''] 158 [82, 'B', 66, ''] 159 [82, 'B', 67, ''] 160 [82, 'B', 68, ''] 161 [82, 'B', 69, ''] 162 [82, 'B', 70, ''] 163 [82, 'B', 71, ''] 164 [82, 'B', 72, ''] 165 [82, 'B', 73, ''] 166 [82, 'B', 74, ''] 167 [82, 'B', 75, ''] 168 [82, 'B', 76, ''] 169 [82, 'B', 77, ''] 170 [82, 'B', 78, ''] 171 [82, 'B', 79, ''] 172 [82, 'B', 80, ''] 173 [82, 'B', 81, ''] 174 [82, 'B', 82, ''] 175 [82, 'B', 83, ''] 176 [82, 'B', 84, ''] 177 [82, 'B', 85, ''] 178 [82, 'B', 86, ''] 179 [82, 'B', 87, ''] 180 [82, 'B', 88, ''] 181 [82, 'B', 89, ''] 182 [82, 'B', 90, ''] 183 [82, 'B', 91, ''] 184 [82, 'B', 92, ''] 185 [82, 'B', 93, ''] 186 [82, 'B', 94, ''] 187 [82, 'B', 95, ''] 188 [82, 'B', 96, ''] ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 83 read successfully DEBUG:: there were 0 types with no dictionary specs: 189 [[83, 'A', 1, ''], [83, 'A', 2, ''], [83, 'A', 3, ''], [83, 'A', 4, ''], [83, 'A', 5, ''], [83, 'A', 6, ''], [83, 'A', 7, ''], [83, 'A', 8, ''], [83, 'A', 9, ''], [83, 'A', 10, ''], [83, 'A', 11, ''], [83, 'A', 12, ''], [83, 'A', 13, ''], [83, 'A', 14, ''], [83, 'A', 15, ''], [83, 'A', 16, ''], [83, 'A', 17, ''], [83, 'A', 18, ''], [83, 'A', 19, ''], [83, 'A', 20, ''], [83, 'A', 21, ''], [83, 'A', 22, ''], [83, 'A', 23, ''], [83, 'A', 24, ''], [83, 'A', 25, ''], [83, 'A', 26, ''], [83, 'A', 27, ''], [83, 'A', 28, ''], [83, 'A', 29, ''], [83, 'A', 30, ''], [83, 'A', 31, ''], [83, 'A', 32, ''], [83, 'A', 33, ''], [83, 'A', 34, ''], [83, 'A', 35, ''], [83, 'A', 36, ''], [83, 'A', 37, ''], [83, 'A', 38, ''], [83, 'A', 39, ''], [83, 'A', 40, ''], [83, 'A', 41, ''], [83, 'A', 42, ''], [83, 'A', 43, ''], [83, 'A', 44, ''], [83, 'A', 45, ''], [83, 'A', 46, ''], [83, 'A', 47, ''], [83, 'A', 48, ''], [83, 'A', 49, ''], [83, 'A', 50, ''], [83, 'A', 51, ''], [83, 'A', 52, ''], [83, 'A', 53, ''], [83, 'A', 54, ''], [83, 'A', 55, ''], [83, 'A', 56, ''], [83, 'A', 57, ''], [83, 'A', 58, ''], [83, 'A', 59, ''], [83, 'A', 60, ''], [83, 'A', 61, ''], [83, 'A', 62, ''], [83, 'A', 63, ''], [83, 'A', 64, ''], [83, 'A', 65, ''], [83, 'A', 66, ''], [83, 'A', 67, ''], [83, 'A', 68, ''], [83, 'A', 69, ''], [83, 'A', 70, ''], [83, 'A', 71, ''], [83, 'A', 72, ''], [83, 'A', 73, ''], [83, 'A', 74, ''], [83, 'A', 75, ''], [83, 'A', 76, ''], [83, 'A', 77, ''], [83, 'A', 78, ''], [83, 'A', 79, ''], [83, 'A', 80, ''], [83, 'A', 81, ''], [83, 'A', 82, ''], [83, 'A', 83, ''], [83, 'A', 84, ''], [83, 'A', 85, ''], [83, 'A', 86, ''], [83, 'A', 87, ''], [83, 'A', 88, ''], [83, 'A', 89, ''], [83, 'A', 90, ''], [83, 'A', 91, ''], [83, 'A', 92, ''], [83, 'A', 93, ''], [83, 'B', 1, ''], [83, 'B', 2, ''], [83, 'B', 3, ''], [83, 'B', 4, ''], [83, 'B', 5, ''], [83, 'B', 6, ''], [83, 'B', 7, ''], [83, 'B', 8, ''], [83, 'B', 9, ''], [83, 'B', 10, ''], [83, 'B', 11, ''], [83, 'B', 12, ''], [83, 'B', 13, ''], [83, 'B', 14, ''], [83, 'B', 15, ''], [83, 'B', 16, ''], [83, 'B', 17, ''], [83, 'B', 18, ''], [83, 'B', 19, ''], [83, 'B', 20, ''], [83, 'B', 21, ''], [83, 'B', 22, ''], [83, 'B', 23, ''], [83, 'B', 24, ''], [83, 'B', 25, ''], [83, 'B', 26, ''], [83, 'B', 27, ''], [83, 'B', 28, ''], [83, 'B', 29, ''], [83, 'B', 30, ''], [83, 'B', 31, ''], [83, 'B', 32, ''], [83, 'B', 33, ''], [83, 'B', 34, ''], [83, 'B', 35, ''], [83, 'B', 36, ''], [83, 'B', 37, ''], [83, 'B', 38, ''], [83, 'B', 39, ''], [83, 'B', 40, ''], [83, 'B', 41, ''], [83, 'B', 42, ''], [83, 'B', 43, ''], [83, 'B', 44, ''], [83, 'B', 45, ''], [83, 'B', 46, ''], [83, 'B', 47, ''], [83, 'B', 48, ''], [83, 'B', 49, ''], [83, 'B', 50, ''], [83, 'B', 51, ''], [83, 'B', 52, ''], [83, 'B', 53, ''], [83, 'B', 54, ''], [83, 'B', 55, ''], [83, 'B', 56, ''], [83, 'B', 57, ''], [83, 'B', 58, ''], [83, 'B', 59, ''], [83, 'B', 60, ''], [83, 'B', 61, ''], [83, 'B', 62, ''], [83, 'B', 63, ''], [83, 'B', 64, ''], [83, 'B', 65, ''], [83, 'B', 66, ''], [83, 'B', 67, ''], [83, 'B', 68, ''], [83, 'B', 69, ''], [83, 'B', 70, ''], [83, 'B', 71, ''], [83, 'B', 72, ''], [83, 'B', 73, ''], [83, 'B', 74, ''], [83, 'B', 75, ''], [83, 'B', 76, ''], [83, 'B', 77, ''], [83, 'B', 78, ''], [83, 'B', 79, ''], [83, 'B', 80, ''], [83, 'B', 81, ''], [83, 'B', 82, ''], [83, 'B', 83, ''], [83, 'B', 84, ''], [83, 'B', 85, ''], [83, 'B', 86, ''], [83, 'B', 87, ''], [83, 'B', 88, ''], [83, 'B', 89, ''], [83, 'B', 90, ''], [83, 'B', 91, ''], [83, 'B', 92, ''], [83, 'B', 93, ''], [83, 'B', 94, ''], [83, 'B', 95, ''], [83, 'B', 96, '']] ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... Reading coordinate file: /home/emsley/data/greg-data/2goz-manip.pdb PDB file /home/emsley/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links Symmetry available for this molecule INFO:: NCS chain comparison 10/85 Molecule 84 read successfully DEBUG:: there were 7 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "GDP" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GDP.cif INFO:: using standard CCP4 Refmac dictionary to search for "Gr" INFO:: using standard CCP4 Refmac dictionary to search for "Ar" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif INFO:: using standard CCP4 Refmac dictionary to search for "Ur" INFO:: using standard CCP4 Refmac dictionary to search for "Cr" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif INFO:: using standard CCP4 Refmac dictionary to search for "OMC" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/o/OMC.cif INFO:: using standard CCP4 Refmac dictionary to search for "5BU" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/5/5BU.cif ok test98_0 (__main__.PdbMtzTestFunctions) Hundreds of Ramachandran refinements (post_manipulation_hook_py test) ... There are 93 residues in chain A centering on A 1 CA created 13 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: 1.66113e+07 Initial RMS Z values bonds: 1022.99 angles: 22.9293 torsions: N/A planes: 7.96279 non-bonded: 0 chiral vol: 671.756 rama plot: N/A start_pos: N/A Minimum found (iteration number 357) at -195.689 Final Estimated RMS Z Scores: bonds: 0.175004 angles: 0.5122 torsions: N/A planes: 1.02503 non-bonded: 0.000128865 chiral vol: 0.126352 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 35.046 Refinement elapsed time: 0.108 INFO:: replace_coords: 15 atoms updated. centering on A 2 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 1 and 3 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -318.052 Initial RMS Z values bonds: 0.44855 angles: 0.801564 torsions: N/A planes: 0.94402 non-bonded: 5.67725e-05 chiral vol: 0.888401 rama plot: -17.722 start_pos: N/A Minimum found (iteration number 388) at -362.421 Final Estimated RMS Z Scores: bonds: 0.113553 angles: 0.774053 torsions: N/A planes: 1.12746 non-bonded: 0.000322985 chiral vol: 0.571655 rama plot: -52.5579 start_pos: N/A SUCCESS TIME:: (dragged refinement): 35.76 Refinement elapsed time: 0.14 INFO:: replace_coords: 21 atoms updated. centering on A 3 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 2 and 4 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -655.675 Initial RMS Z values bonds: 0.17483 angles: 0.959585 torsions: N/A planes: 1.06446 non-bonded: 0.0120683 chiral vol: 0.70006 rama plot: -101.702 start_pos: N/A Minimum found (iteration number 185) at -734.992 Final Estimated RMS Z Scores: bonds: 0.192136 angles: 0.731678 torsions: N/A planes: 0.936847 non-bonded: 0 chiral vol: 0.720181 rama plot: -129.265 start_pos: N/A SUCCESS TIME:: (dragged refinement): 36.316 Refinement elapsed time: 0.07 INFO:: replace_coords: 17 atoms updated. centering on A 4 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 3 and 5 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -898.626 Initial RMS Z values bonds: 0.490804 angles: 1.22154 torsions: N/A planes: 0.939183 non-bonded: 0 chiral vol: 0.935274 rama plot: -169.876 start_pos: N/A Minimum found (iteration number 260) at -940.25 Final Estimated RMS Z Scores: bonds: 0.172497 angles: 0.451628 torsions: N/A planes: 0.966358 non-bonded: 0 chiral vol: 0.508247 rama plot: -172.317 start_pos: N/A SUCCESS TIME:: (dragged refinement): 36.865 Refinement elapsed time: 0.033 INFO:: replace_coords: 17 atoms updated. centering on A 5 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 4 and 6 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1013.76 Initial RMS Z values bonds: 0.786713 angles: 0.70451 torsions: N/A planes: 0.780233 non-bonded: 0 chiral vol: 0.32636 rama plot: -157.943 start_pos: N/A Minimum found (iteration number 224) at -1038.07 Final Estimated RMS Z Scores: bonds: 0.229527 angles: 0.438818 torsions: N/A planes: 0.531027 non-bonded: 0 chiral vol: 0.176065 rama plot: -159.35 start_pos: N/A SUCCESS TIME:: (dragged refinement): 37.499 Refinement elapsed time: 0.032 INFO:: replace_coords: 18 atoms updated. centering on A 6 CA created 17 bond restraints created 19 angle restraints created 0 plane restraints created 4 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 5 and 7 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1373.12 Initial RMS Z values bonds: 0.866928 angles: 0.764435 torsions: N/A planes: 0.533115 non-bonded: 0 chiral vol: 0.294055 rama plot: -182.318 start_pos: N/A Minimum found (iteration number 268) at -1401.43 Final Estimated RMS Z Scores: bonds: 0.253411 angles: 0.364998 torsions: N/A planes: 0.477332 non-bonded: 0 chiral vol: 0.153497 rama plot: -182.586 start_pos: N/A SUCCESS TIME:: (dragged refinement): 38.159 Refinement elapsed time: 0.038 INFO:: replace_coords: 20 atoms updated. centering on A 7 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 6 and 8 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1483.39 Initial RMS Z values bonds: 0.657971 angles: 0.632174 torsions: N/A planes: 0.868444 non-bonded: 0 chiral vol: 0.713248 rama plot: -189.337 start_pos: N/A Minimum found (iteration number 292) at -1520.52 Final Estimated RMS Z Scores: bonds: 0.269147 angles: 0.277825 torsions: N/A planes: 0.751019 non-bonded: 0 chiral vol: 0.192693 rama plot: -194.6 start_pos: N/A SUCCESS TIME:: (dragged refinement): 38.819 Refinement elapsed time: 0.042 INFO:: replace_coords: 21 atoms updated. centering on A 8 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 3 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 7 and 9 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1484.81 Initial RMS Z values bonds: 0.494284 angles: 0.678836 torsions: N/A planes: 0.824488 non-bonded: 0 chiral vol: 0.483887 rama plot: -197.057 start_pos: N/A Minimum found (iteration number 279) at -1511.29 Final Estimated RMS Z Scores: bonds: 0.222686 angles: 0.408698 torsions: N/A planes: 0.548012 non-bonded: 0 chiral vol: 0.216047 rama plot: -201.596 start_pos: N/A SUCCESS TIME:: (dragged refinement): 39.494 Refinement elapsed time: 0.04 INFO:: replace_coords: 20 atoms updated. centering on A 9 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 8 and 10 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1152.29 Initial RMS Z values bonds: 0.445734 angles: 0.735409 torsions: N/A planes: 3.38172 non-bonded: 0 chiral vol: 0.586137 rama plot: -199.949 start_pos: N/A Minimum found (iteration number 312) at -1246.12 Final Estimated RMS Z Scores: bonds: 0.150483 angles: 0.49841 torsions: N/A planes: 1.7173 non-bonded: 0 chiral vol: 0.219144 rama plot: -213.812 start_pos: N/A SUCCESS TIME:: (dragged refinement): 40.078 Refinement elapsed time: 0.042 INFO:: replace_coords: 19 atoms updated. centering on A 10 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 9 and 11 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 4035.75 Initial RMS Z values bonds: 13.5293 angles: 6.91676 torsions: N/A planes: 2.02785 non-bonded: 0 chiral vol: 5.81366 rama plot: -184.768 start_pos: N/A Minimum found (iteration number 369) at -1204.01 Final Estimated RMS Z Scores: bonds: 0.316637 angles: 0.561557 torsions: N/A planes: 0.588642 non-bonded: 0 chiral vol: 0.470511 rama plot: -204.638 start_pos: N/A SUCCESS TIME:: (dragged refinement): 40.638 Refinement elapsed time: 0.054 INFO:: replace_coords: 19 atoms updated. centering on A 11 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 10 and 12 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -589.442 Initial RMS Z values bonds: 1.02008 angles: 0.711171 torsions: N/A planes: 0.653209 non-bonded: 1.85436 chiral vol: 0.569213 rama plot: -179.016 start_pos: N/A Minimum found (iteration number 2) at -1028.47 Final Estimated RMS Z Scores: bonds: 1.66921 angles: 1.18212 torsions: N/A planes: 0.792969 non-bonded: 0.11807 chiral vol: 0.39277 rama plot: -190.435 start_pos: N/A SUCCESS TIME:: (dragged refinement): 41.256 Refinement elapsed time: 0.057 INFO:: replace_coords: 20 atoms updated. centering on A 12 CA created 21 bond restraints created 24 angle restraints created 0 plane restraints created 3 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 11 and 13 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -477.439 Initial RMS Z values bonds: 1.70161 angles: 1.14531 torsions: N/A planes: 0.859162 non-bonded: 1.95349 chiral vol: 0.406311 rama plot: -181.581 start_pos: N/A Minimum found (iteration number 392) at -939.289 Final Estimated RMS Z Scores: bonds: 2.15659 angles: 1.55285 torsions: N/A planes: 0.790874 non-bonded: 0.210016 chiral vol: 0.254165 rama plot: -184.318 start_pos: N/A SUCCESS TIME:: (dragged refinement): 41.835 Refinement elapsed time: 0.059 INFO:: replace_coords: 22 atoms updated. centering on A 13 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 3 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 12 and 14 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1050.11 Initial RMS Z values bonds: 2.16537 angles: 1.65817 torsions: N/A planes: 0.861209 non-bonded: 0.0827184 chiral vol: 0.510986 rama plot: -191.951 start_pos: N/A Minimum found (iteration number 385) at -1181.31 Final Estimated RMS Z Scores: bonds: 1.50399 angles: 1.13464 torsions: N/A planes: 0.670951 non-bonded: 0.0820513 chiral vol: 0.114191 rama plot: -196.23 start_pos: N/A SUCCESS TIME:: (dragged refinement): 42.437 Refinement elapsed time: 0.061 INFO:: replace_coords: 23 atoms updated. centering on A 14 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 13 and 15 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1201.87 Initial RMS Z values bonds: 1.89106 angles: 1.31564 torsions: N/A planes: 1.00526 non-bonded: 0 chiral vol: 1.08684 rama plot: -208.831 start_pos: N/A Minimum found (iteration number 2) at -1353.52 Final Estimated RMS Z Scores: bonds: 0.185893 angles: 0.359181 torsions: N/A planes: 0.846377 non-bonded: 0 chiral vol: 0.0914935 rama plot: -212.093 start_pos: N/A SUCCESS TIME:: (dragged refinement): 43.102 Refinement elapsed time: 0.055 INFO:: replace_coords: 21 atoms updated. centering on A 15 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 14 and 16 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1382.17 Initial RMS Z values bonds: 0.698517 angles: 0.966919 torsions: N/A planes: 0.825763 non-bonded: 0 chiral vol: 0.575222 rama plot: -213.281 start_pos: N/A Minimum found (iteration number 245) at -1437.58 Final Estimated RMS Z Scores: bonds: 0.130638 angles: 0.276026 torsions: N/A planes: 0.508037 non-bonded: 0 chiral vol: 0.165984 rama plot: -217.895 start_pos: N/A SUCCESS TIME:: (dragged refinement): 43.826 Refinement elapsed time: 0.036 INFO:: replace_coords: 21 atoms updated. centering on A 16 CA created 17 bond restraints created 19 angle restraints created 1 plane restraints created 4 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 15 and 17 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1431.3 Initial RMS Z values bonds: 0.717313 angles: 0.679966 torsions: N/A planes: 1.01114 non-bonded: 0 chiral vol: 0.198972 rama plot: -217.987 start_pos: N/A Minimum found (iteration number 236) at -1469.23 Final Estimated RMS Z Scores: bonds: 0.117296 angles: 0.297148 torsions: N/A planes: 0.314621 non-bonded: 0 chiral vol: 0.167215 rama plot: -220.867 start_pos: N/A SUCCESS TIME:: (dragged refinement): 44.554 Refinement elapsed time: 0.035 INFO:: replace_coords: 20 atoms updated. centering on A 17 CA created 19 bond restraints created 22 angle restraints created 1 plane restraints created 5 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 16 and 18 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1524.19 Initial RMS Z values bonds: 0.653112 angles: 0.846194 torsions: N/A planes: 0.504815 non-bonded: 0 chiral vol: 0.401675 rama plot: -217.857 start_pos: N/A Minimum found (iteration number 235) at -1559.34 Final Estimated RMS Z Scores: bonds: 0.135195 angles: 0.388528 torsions: N/A planes: 0.40414 non-bonded: 0 chiral vol: 0.284667 rama plot: -220.098 start_pos: N/A SUCCESS TIME:: (dragged refinement): 45.277 Refinement elapsed time: 0.037 INFO:: replace_coords: 22 atoms updated. centering on A 18 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 17 and 19 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1537.45 Initial RMS Z values bonds: 0.625823 angles: 0.561889 torsions: N/A planes: 0.352159 non-bonded: 0 chiral vol: 0.374284 rama plot: -216.736 start_pos: N/A Minimum found (iteration number 286) at -1567 Final Estimated RMS Z Scores: bonds: 0.127147 angles: 0.313199 torsions: N/A planes: 0.24547 non-bonded: 0 chiral vol: 0.210993 rama plot: -220.181 start_pos: N/A SUCCESS TIME:: (dragged refinement): 46.004 Refinement elapsed time: 0.042 INFO:: replace_coords: 23 atoms updated. centering on A 19 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 18 and 20 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1469.43 Initial RMS Z values bonds: 0.414026 angles: 0.570268 torsions: N/A planes: 0.844639 non-bonded: 0 chiral vol: 0.13424 rama plot: -217.854 start_pos: N/A Minimum found (iteration number 325) at -1499.19 Final Estimated RMS Z Scores: bonds: 0.13075 angles: 0.282027 torsions: N/A planes: 0.21195 non-bonded: 0 chiral vol: 0.142155 rama plot: -221.306 start_pos: N/A SUCCESS TIME:: (dragged refinement): 46.819 Refinement elapsed time: 0.051 INFO:: replace_coords: 23 atoms updated. centering on A 20 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 19 and 21 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1456.13 Initial RMS Z values bonds: 0.861175 angles: 0.476066 torsions: N/A planes: 0.267076 non-bonded: 0 chiral vol: 0.398234 rama plot: -219.659 start_pos: N/A Minimum found (iteration number 327) at -1485.27 Final Estimated RMS Z Scores: bonds: 0.131814 angles: 0.234471 torsions: N/A planes: 0.276947 non-bonded: 0 chiral vol: 0.150565 rama plot: -221.383 start_pos: N/A SUCCESS TIME:: (dragged refinement): 47.56 Refinement elapsed time: 0.054 INFO:: replace_coords: 24 atoms updated. centering on A 21 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 20 and 22 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1387.11 Initial RMS Z values bonds: 0.76735 angles: 0.584829 torsions: N/A planes: 1.06665 non-bonded: 0.102406 chiral vol: 0.244094 rama plot: -221.037 start_pos: N/A Minimum found (iteration number 292) at -1456.43 Final Estimated RMS Z Scores: bonds: 0.149852 angles: 0.236978 torsions: N/A planes: 0.71267 non-bonded: 9.22745e-06 chiral vol: 0.162724 rama plot: -221.059 start_pos: N/A SUCCESS TIME:: (dragged refinement): 48.231 Refinement elapsed time: 0.05 INFO:: replace_coords: 24 atoms updated. centering on A 22 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 4 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 21 and 23 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1323.44 Initial RMS Z values bonds: 0.552551 angles: 0.482038 torsions: N/A planes: 0.880624 non-bonded: 1.22821e-05 chiral vol: 0.163615 rama plot: -214.828 start_pos: N/A Minimum found (iteration number 288) at -1357.59 Final Estimated RMS Z Scores: bonds: 0.133081 angles: 0.226297 torsions: N/A planes: 0.452317 non-bonded: 1.98703e-05 chiral vol: 0.127261 rama plot: -221.21 start_pos: N/A SUCCESS TIME:: (dragged refinement): 48.922 Refinement elapsed time: 0.042 INFO:: replace_coords: 21 atoms updated. centering on A 23 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 4 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 22 and 24 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1195.01 Initial RMS Z values bonds: 0.46194 angles: 0.530971 torsions: N/A planes: 0.864102 non-bonded: 2.46256e-05 chiral vol: 0.0695084 rama plot: -204.97 start_pos: N/A Minimum found (iteration number 311) at -1205.96 Final Estimated RMS Z Scores: bonds: 0.14671 angles: 0.306055 torsions: N/A planes: 0.842249 non-bonded: 9.09977e-06 chiral vol: 0.098276 rama plot: -205.644 start_pos: N/A SUCCESS TIME:: (dragged refinement): 49.634 Refinement elapsed time: 0.046 INFO:: replace_coords: 19 atoms updated. centering on A 24 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 23 and 25 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1010.96 Initial RMS Z values bonds: 0.553533 angles: 0.864892 torsions: N/A planes: 1.17525 non-bonded: 0 chiral vol: 0.294591 rama plot: -182.217 start_pos: N/A Minimum found (iteration number 155) at -1051.09 Final Estimated RMS Z Scores: bonds: 0.106656 angles: 0.210975 torsions: N/A planes: 0.742159 non-bonded: 0 chiral vol: 0.119839 rama plot: -184.962 start_pos: N/A SUCCESS TIME:: (dragged refinement): 50.237 Refinement elapsed time: 0.073 INFO:: replace_coords: 19 atoms updated. centering on A 25 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 24 and 26 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -884.286 Initial RMS Z values bonds: 0.227907 angles: 0.264624 torsions: N/A planes: 0.917474 non-bonded: 0 chiral vol: 0.145102 rama plot: -149.172 start_pos: N/A Minimum found (iteration number 244) at -892.559 Final Estimated RMS Z Scores: bonds: 0.141926 angles: 0.191745 torsions: N/A planes: 0.706235 non-bonded: 0 chiral vol: 0.114535 rama plot: -150.258 start_pos: N/A SUCCESS TIME:: (dragged refinement): 50.778 Refinement elapsed time: 0.033 INFO:: replace_coords: 18 atoms updated. centering on A 26 CA created 17 bond restraints created 18 angle restraints created 1 plane restraints created 2 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 25 and 27 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -153.412 Initial RMS Z values bonds: 0.653866 angles: 0.511831 torsions: N/A planes: 0.913917 non-bonded: 3.17035 chiral vol: 0.122652 rama plot: -147.801 start_pos: N/A Minimum found (iteration number 158) at -701.413 Final Estimated RMS Z Scores: bonds: 1.88009 angles: 1.15414 torsions: N/A planes: 0.716745 non-bonded: 0.165725 chiral vol: 0.243109 rama plot: -149.749 start_pos: N/A SUCCESS TIME:: (dragged refinement): 51.361 Refinement elapsed time: 0.073 INFO:: replace_coords: 19 atoms updated. centering on A 27 CA created 21 bond restraints created 23 angle restraints created 1 plane restraints created 2 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 26 and 28 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -816.996 Initial RMS Z values bonds: 1.91267 angles: 1.15042 torsions: N/A planes: 1.00607 non-bonded: 0.100753 chiral vol: 0.244685 rama plot: -154.678 start_pos: N/A Minimum found (iteration number 400) at -855.922 Final Estimated RMS Z Scores: bonds: 1.72201 angles: 1.08048 torsions: N/A planes: 0.424863 non-bonded: 0.101228 chiral vol: 0.196931 rama plot: -157.369 start_pos: N/A SUCCESS TIME:: (dragged refinement): 51.934 Refinement elapsed time: 0.063 INFO:: replace_coords: 22 atoms updated. centering on A 28 CA created 25 bond restraints created 29 angle restraints created 1 plane restraints created 3 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 27 and 29 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -332.594 Initial RMS Z values bonds: 1.85885 angles: 1.11625 torsions: N/A planes: 0.40024 non-bonded: 1.62853 chiral vol: 0.827291 rama plot: -181.069 start_pos: N/A Minimum found (iteration number 73) at -1034.69 Final Estimated RMS Z Scores: bonds: 1.42909 angles: 1.04687 torsions: N/A planes: 0.742243 non-bonded: 0.0801861 chiral vol: 0.280785 rama plot: -188.307 start_pos: N/A SUCCESS TIME:: (dragged refinement): 52.569 Refinement elapsed time: 0.084 INFO:: replace_coords: 25 atoms updated. centering on A 29 CA created 30 bond restraints created 36 angle restraints created 2 plane restraints created 3 chiral vol restraints created 71 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 28 and 30 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1172.8 Initial RMS Z values bonds: 1.47363 angles: 1.06888 torsions: N/A planes: 1.24883 non-bonded: 0.06207 chiral vol: 0.519281 rama plot: -187.206 start_pos: N/A Minimum found (iteration number 398) at -1219.07 Final Estimated RMS Z Scores: bonds: 1.33429 angles: 0.932298 torsions: N/A planes: 0.510448 non-bonded: 0.0621339 chiral vol: 0.332117 rama plot: -189.713 start_pos: N/A SUCCESS TIME:: (dragged refinement): 53.231 Refinement elapsed time: 0.078 INFO:: replace_coords: 30 atoms updated. centering on A 30 CA created 24 bond restraints created 28 angle restraints created 1 plane restraints created 3 chiral vol restraints created 56 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 29 and 31 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1087.56 Initial RMS Z values bonds: 1.48634 angles: 1.42284 torsions: N/A planes: 0.525108 non-bonded: 0 chiral vol: 0.479635 rama plot: -203.558 start_pos: N/A Minimum found (iteration number 320) at -1232.31 Final Estimated RMS Z Scores: bonds: 0.159064 angles: 0.395056 torsions: N/A planes: 0.489801 non-bonded: 0 chiral vol: 0.147601 rama plot: -206.027 start_pos: N/A SUCCESS TIME:: (dragged refinement): 54.007 Refinement elapsed time: 0.169 INFO:: replace_coords: 25 atoms updated. centering on A 31 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 30 and 32 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1045.94 Initial RMS Z values bonds: 1.35056 angles: 0.903031 torsions: N/A planes: 0.775111 non-bonded: 0 chiral vol: 0.935559 rama plot: -190.719 start_pos: N/A Minimum found (iteration number 304) at -1163.71 Final Estimated RMS Z Scores: bonds: 0.134846 angles: 0.27749 torsions: N/A planes: 0.746548 non-bonded: 0 chiral vol: 0.145597 rama plot: -203.992 start_pos: N/A SUCCESS TIME:: (dragged refinement): 54.719 Refinement elapsed time: 0.121 INFO:: replace_coords: 27 atoms updated. centering on A 32 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 3 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 31 and 33 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1021.23 Initial RMS Z values bonds: 0.387346 angles: 0.648823 torsions: N/A planes: 0.691984 non-bonded: 0.127753 chiral vol: 0.371734 rama plot: -192.404 start_pos: N/A Minimum found (iteration number 256) at -1113.67 Final Estimated RMS Z Scores: bonds: 0.111382 angles: 0.433654 torsions: N/A planes: 0.609095 non-bonded: 0 chiral vol: 0.30155 rama plot: -201.448 start_pos: N/A SUCCESS TIME:: (dragged refinement): 55.438 Refinement elapsed time: 0.098 INFO:: replace_coords: 23 atoms updated. centering on A 33 CA created 18 bond restraints created 19 angle restraints created 2 plane restraints created 2 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 32 and 34 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1051.99 Initial RMS Z values bonds: 0.376094 angles: 0.677091 torsions: N/A planes: 0.975452 non-bonded: 0 chiral vol: 0.345594 rama plot: -176.51 start_pos: N/A Minimum found (iteration number 71) at -1063.34 Final Estimated RMS Z Scores: bonds: 0.174043 angles: 0.698969 torsions: N/A planes: 1.07777 non-bonded: 0 chiral vol: 0.288736 rama plot: -180.716 start_pos: N/A SUCCESS TIME:: (dragged refinement): 56.117 Refinement elapsed time: 0.072 INFO:: replace_coords: 21 atoms updated. centering on A 34 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 33 and 35 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1087.39 Initial RMS Z values bonds: 0.800596 angles: 0.63094 torsions: N/A planes: 1.08231 non-bonded: 0 chiral vol: 0.319111 rama plot: -162.572 start_pos: N/A Minimum found (iteration number 290) at -1131.09 Final Estimated RMS Z Scores: bonds: 0.189232 angles: 0.470651 torsions: N/A planes: 0.906516 non-bonded: 0 chiral vol: 0.123439 rama plot: -171.061 start_pos: N/A SUCCESS TIME:: (dragged refinement): 56.777 Refinement elapsed time: 0.039 INFO:: replace_coords: 19 atoms updated. centering on A 35 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 34 and 36 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1070.96 Initial RMS Z values bonds: 0.927349 angles: 0.536562 torsions: N/A planes: 0.968818 non-bonded: 0 chiral vol: 0.165404 rama plot: -171.787 start_pos: N/A Minimum found (iteration number 284) at -1095.32 Final Estimated RMS Z Scores: bonds: 0.124344 angles: 0.397919 torsions: N/A planes: 0.835506 non-bonded: 0 chiral vol: 0.131334 rama plot: -172.819 start_pos: N/A SUCCESS TIME:: (dragged refinement): 57.499 Refinement elapsed time: 0.038 INFO:: replace_coords: 18 atoms updated. centering on A 36 CA created 23 bond restraints created 27 angle restraints created 1 plane restraints created 3 chiral vol restraints created 54 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 35 and 37 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1288.41 Initial RMS Z values bonds: 0.796606 angles: 0.564389 torsions: N/A planes: 1.35999 non-bonded: 0 chiral vol: 0.311258 rama plot: -181.299 start_pos: N/A Minimum found (iteration number 323) at -1313.51 Final Estimated RMS Z Scores: bonds: 0.138664 angles: 0.437053 torsions: N/A planes: 1.18042 non-bonded: 0 chiral vol: 0.453783 rama plot: -181.973 start_pos: N/A SUCCESS TIME:: (dragged refinement): 58.237 Refinement elapsed time: 0.052 INFO:: replace_coords: 25 atoms updated. centering on A 37 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 36 and 38 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1358.11 Initial RMS Z values bonds: 0.502652 angles: 0.825721 torsions: N/A planes: 1.05622 non-bonded: 0 chiral vol: 0.658362 rama plot: -181.264 start_pos: N/A Minimum found (iteration number 360) at -1413.06 Final Estimated RMS Z Scores: bonds: 0.174609 angles: 0.473783 torsions: N/A planes: 0.96723 non-bonded: 5.09118e-06 chiral vol: 0.517909 rama plot: -193.983 start_pos: N/A SUCCESS TIME:: (dragged refinement): 59.021 Refinement elapsed time: 0.064 INFO:: replace_coords: 27 atoms updated. centering on A 38 CA created 26 bond restraints created 30 angle restraints created 3 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 37 and 39 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1448.21 Initial RMS Z values bonds: 0.611751 angles: 0.615961 torsions: N/A planes: 1.11098 non-bonded: 0 chiral vol: 0.766891 rama plot: -181.891 start_pos: N/A Minimum found (iteration number 357) at -1478.1 Final Estimated RMS Z Scores: bonds: 0.159274 angles: 0.47401 torsions: N/A planes: 1.01812 non-bonded: 0 chiral vol: 0.699968 rama plot: -185.012 start_pos: N/A SUCCESS TIME:: (dragged refinement): 59.785 Refinement elapsed time: 0.069 INFO:: replace_coords: 28 atoms updated. centering on A 39 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 38 and 40 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1268.61 Initial RMS Z values bonds: 0.614109 angles: 0.823182 torsions: N/A planes: 3.36808 non-bonded: 0.0133491 chiral vol: 0.716088 rama plot: -196.62 start_pos: N/A Minimum found (iteration number 237) at -1336.91 Final Estimated RMS Z Scores: bonds: 0.198154 angles: 0.612948 torsions: N/A planes: 2.34769 non-bonded: 1.0926e-06 chiral vol: 0.716195 rama plot: -192.543 start_pos: N/A SUCCESS TIME:: (dragged refinement): 60.718 INFO:: found bad chiral atom: A 41 CA There is one residue with an incorrect chiral volume A 41 CA Refinement elapsed time: 0.259 INFO:: replace_coords: 28 atoms updated. centering on A 40 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 39 and 41 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 624.914 Initial RMS Z values bonds: 0.741459 angles: 0.742027 torsions: N/A planes: 3.76283 non-bonded: 1.88076 chiral vol: 13.2459 rama plot: -145.886 start_pos: N/A Minimum found (iteration number 211) at -1119.19 Final Estimated RMS Z Scores: bonds: 0.280235 angles: 1.24636 torsions: N/A planes: 2.27398 non-bonded: 0.000506149 chiral vol: 1.14499 rama plot: -178.392 start_pos: N/A SUCCESS TIME:: (dragged refinement): 61.574 Refinement elapsed time: 0.182 INFO:: replace_coords: 28 atoms updated. centering on A 41 CA created 23 bond restraints created 25 angle restraints created 2 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 40 and 42 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -917.417 Initial RMS Z values bonds: 0.32017 angles: 1.33442 torsions: N/A planes: 2.33355 non-bonded: 0.000510611 chiral vol: 1.16722 rama plot: -145.96 start_pos: N/A Minimum found (iteration number 391) at -969.015 Final Estimated RMS Z Scores: bonds: 0.291601 angles: 1.21164 torsions: N/A planes: 2.41627 non-bonded: 0.000669162 chiral vol: 1.14273 rama plot: -164.08 start_pos: N/A SUCCESS TIME:: (dragged refinement): 62.309 Refinement elapsed time: 0.068 INFO:: replace_coords: 26 atoms updated. centering on A 42 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 41 and 43 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -936.525 Initial RMS Z values bonds: 0.424375 angles: 1.19596 torsions: N/A planes: 2.53847 non-bonded: 0.000177118 chiral vol: 0.921655 rama plot: -154.476 start_pos: N/A Minimum found (iteration number 156) at -989.965 Final Estimated RMS Z Scores: bonds: 0.258517 angles: 0.753638 torsions: N/A planes: 2.46875 non-bonded: 0.000111092 chiral vol: 0.42173 rama plot: -166.755 start_pos: N/A SUCCESS TIME:: (dragged refinement): 63.098 Refinement elapsed time: 0.082 INFO:: replace_coords: 22 atoms updated. centering on A 43 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 42 and 44 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1217.05 Initial RMS Z values bonds: 0.624207 angles: 0.701227 torsions: N/A planes: 1.13982 non-bonded: 0 chiral vol: 0.324523 rama plot: -177.22 start_pos: N/A Minimum found (iteration number 310) at -1242.97 Final Estimated RMS Z Scores: bonds: 0.216416 angles: 0.577263 torsions: N/A planes: 0.983364 non-bonded: 0 chiral vol: 0.125732 rama plot: -181.358 start_pos: N/A SUCCESS TIME:: (dragged refinement): 63.781 Refinement elapsed time: 0.043 INFO:: replace_coords: 21 atoms updated. centering on A 44 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 3 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 43 and 45 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -774.404 Initial RMS Z values bonds: 0.644135 angles: 0.494094 torsions: N/A planes: 1.11666 non-bonded: 1.59447 chiral vol: 0.156033 rama plot: -183.812 start_pos: N/A Minimum found (iteration number 6) at -1194.83 Final Estimated RMS Z Scores: bonds: 1.57642 angles: 1.09762 torsions: N/A planes: 0.621566 non-bonded: 0.101997 chiral vol: 0.243595 rama plot: -192.308 start_pos: N/A SUCCESS TIME:: (dragged refinement): 64.521 Refinement elapsed time: 0.059 INFO:: replace_coords: 22 atoms updated. centering on A 45 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 44 and 46 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1109.14 Initial RMS Z values bonds: 1.75817 angles: 1.28511 torsions: N/A planes: 0.605772 non-bonded: 0.10733 chiral vol: 0.36948 rama plot: -174.173 start_pos: N/A Minimum found (iteration number 278) at -1149.73 Final Estimated RMS Z Scores: bonds: 1.5744 angles: 1.10814 torsions: N/A planes: 0.547981 non-bonded: 0.107131 chiral vol: 0.316652 rama plot: -178.393 start_pos: N/A SUCCESS TIME:: (dragged refinement): 65.274 Refinement elapsed time: 0.043 INFO:: replace_coords: 22 atoms updated. centering on A 46 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 45 and 47 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1170.94 Initial RMS Z values bonds: 1.71242 angles: 1.26819 torsions: N/A planes: 0.88193 non-bonded: 0 chiral vol: 0.701422 rama plot: -173.887 start_pos: N/A Minimum found (iteration number 333) at -1318.02 Final Estimated RMS Z Scores: bonds: 0.154774 angles: 0.381382 torsions: N/A planes: 0.457773 non-bonded: 1.19401e-05 chiral vol: 0.174978 rama plot: -177.002 start_pos: N/A SUCCESS TIME:: (dragged refinement): 66.062 Refinement elapsed time: 0.054 INFO:: replace_coords: 23 atoms updated. centering on A 47 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 46 and 48 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1237.67 Initial RMS Z values bonds: 0.805149 angles: 0.575349 torsions: N/A planes: 0.689653 non-bonded: 1.39059e-05 chiral vol: 0.315089 rama plot: -165.761 start_pos: N/A Minimum found (iteration number 293) at -1287.63 Final Estimated RMS Z Scores: bonds: 0.126829 angles: 0.279265 torsions: N/A planes: 0.436083 non-bonded: 4.00645e-06 chiral vol: 0.0789085 rama plot: -175.279 start_pos: N/A SUCCESS TIME:: (dragged refinement): 66.848 Refinement elapsed time: 0.045 INFO:: replace_coords: 22 atoms updated. centering on A 48 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 47 and 49 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1380.6 Initial RMS Z values bonds: 0.775459 angles: 0.726173 torsions: N/A planes: 0.891569 non-bonded: 0.0201985 chiral vol: 0.795581 rama plot: -174.52 start_pos: N/A Minimum found (iteration number 329) at -1431.1 Final Estimated RMS Z Scores: bonds: 0.152839 angles: 0.427033 torsions: N/A planes: 0.283504 non-bonded: 5.08003e-06 chiral vol: 0.412953 rama plot: -175.58 start_pos: N/A SUCCESS TIME:: (dragged refinement): 67.625 Refinement elapsed time: 0.059 INFO:: replace_coords: 27 atoms updated. centering on A 49 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 2 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 48 and 50 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1228.69 Initial RMS Z values bonds: 0.407201 angles: 0.594137 torsions: N/A planes: 0.296891 non-bonded: 0.0208109 chiral vol: 0.502027 rama plot: -170.117 start_pos: N/A Minimum found (iteration number 295) at -1252.43 Final Estimated RMS Z Scores: bonds: 0.200771 angles: 0.431717 torsions: N/A planes: 0.45447 non-bonded: 0 chiral vol: 0.322712 rama plot: -172.722 start_pos: N/A SUCCESS TIME:: (dragged refinement): 68.374 Refinement elapsed time: 0.049 INFO:: replace_coords: 22 atoms updated. centering on A 50 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 49 and 51 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1480.26 Initial RMS Z values bonds: 0.734097 angles: 0.550612 torsions: N/A planes: 0.844111 non-bonded: 0.00460016 chiral vol: 0.777336 rama plot: -177.322 start_pos: N/A Minimum found (iteration number 253) at -1542.31 Final Estimated RMS Z Scores: bonds: 0.127596 angles: 0.190868 torsions: N/A planes: 0.606588 non-bonded: 0 chiral vol: 0.231224 rama plot: -186.935 start_pos: N/A SUCCESS TIME:: (dragged refinement): 69.071 Refinement elapsed time: 0.05 INFO:: replace_coords: 28 atoms updated. centering on A 51 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 50 and 52 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1540.35 Initial RMS Z values bonds: 1.00693 angles: 0.400247 torsions: N/A planes: 0.965826 non-bonded: 0 chiral vol: 0.966735 rama plot: -182.87 start_pos: N/A Minimum found (iteration number 241) at -1584.26 Final Estimated RMS Z Scores: bonds: 0.129722 angles: 0.282488 torsions: N/A planes: 0.733275 non-bonded: 0 chiral vol: 0.24809 rama plot: -183.723 start_pos: N/A SUCCESS TIME:: (dragged refinement): 69.768 Refinement elapsed time: 0.048 INFO:: replace_coords: 28 atoms updated. centering on A 52 CA created 34 bond restraints created 42 angle restraints created 3 plane restraints created 3 chiral vol restraints created 82 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 51 and 53 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1793.79 Initial RMS Z values bonds: 0.479472 angles: 0.409999 torsions: N/A planes: 0.962415 non-bonded: 0 chiral vol: 0.530257 rama plot: -190.791 start_pos: N/A Minimum found (iteration number 381) at -1811.14 Final Estimated RMS Z Scores: bonds: 0.136538 angles: 0.244889 torsions: N/A planes: 0.857109 non-bonded: 0 chiral vol: 0.156197 rama plot: -191 start_pos: N/A SUCCESS TIME:: (dragged refinement): 70.534 Refinement elapsed time: 0.09 INFO:: replace_coords: 34 atoms updated. centering on A 53 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 52 and 54 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1577.36 Initial RMS Z values bonds: 0.378753 angles: 0.583176 torsions: N/A planes: 0.908009 non-bonded: 0 chiral vol: 0.435424 rama plot: -176.893 start_pos: N/A Minimum found (iteration number 34) at -1600.59 Final Estimated RMS Z Scores: bonds: 0.152686 angles: 0.314468 torsions: N/A planes: 0.790398 non-bonded: 0 chiral vol: 0.18428 rama plot: -178.354 start_pos: N/A SUCCESS TIME:: (dragged refinement): 71.339 Refinement elapsed time: 0.082 INFO:: replace_coords: 31 atoms updated. centering on A 54 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 53 and 55 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1575.73 Initial RMS Z values bonds: 0.65377 angles: 0.431707 torsions: N/A planes: 0.89916 non-bonded: 0 chiral vol: 0.238815 rama plot: -178.174 start_pos: N/A Minimum found (iteration number 392) at -1603.79 Final Estimated RMS Z Scores: bonds: 0.151706 angles: 0.254765 torsions: N/A planes: 0.699672 non-bonded: 0 chiral vol: 0.0882928 rama plot: -179.586 start_pos: N/A SUCCESS TIME:: (dragged refinement): 72.177 Refinement elapsed time: 0.085 INFO:: replace_coords: 31 atoms updated. centering on A 55 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 54 and 56 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1483.97 Initial RMS Z values bonds: 0.42653 angles: 0.659886 torsions: N/A planes: 1.67498 non-bonded: 0 chiral vol: 0.617379 rama plot: -181.4 start_pos: N/A Minimum found (iteration number 231) at -1513.15 Final Estimated RMS Z Scores: bonds: 0.159602 angles: 0.260058 torsions: N/A planes: 1.40028 non-bonded: 0 chiral vol: 0.0759561 rama plot: -181.42 start_pos: N/A SUCCESS TIME:: (dragged refinement): 72.922 Refinement elapsed time: 0.047 INFO:: replace_coords: 28 atoms updated. centering on A 56 CA created 24 bond restraints created 29 angle restraints created 1 plane restraints created 4 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 55 and 57 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1480.14 Initial RMS Z values bonds: 0.48613 angles: 0.615557 torsions: N/A planes: 1.47968 non-bonded: 0 chiral vol: 0.406249 rama plot: -180.085 start_pos: N/A Minimum found (iteration number 248) at -1491.3 Final Estimated RMS Z Scores: bonds: 0.198216 angles: 0.514758 torsions: N/A planes: 1.43773 non-bonded: 0 chiral vol: 0.433626 rama plot: -180.174 start_pos: N/A SUCCESS TIME:: (dragged refinement): 73.632 Refinement elapsed time: 0.042 INFO:: replace_coords: 26 atoms updated. centering on A 57 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 56 and 58 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1230.23 Initial RMS Z values bonds: 1.46734 angles: 0.741496 torsions: N/A planes: 1.71934 non-bonded: 0.0985785 chiral vol: 0.600202 rama plot: -181.033 start_pos: N/A Minimum found (iteration number 318) at -1327.16 Final Estimated RMS Z Scores: bonds: 0.21605 angles: 0.501967 torsions: N/A planes: 1.57877 non-bonded: 0.000164683 chiral vol: 0.350192 rama plot: -181.142 start_pos: N/A SUCCESS TIME:: (dragged refinement): 74.328 Refinement elapsed time: 0.047 INFO:: replace_coords: 22 atoms updated. centering on A 58 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 57 and 59 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1233.22 Initial RMS Z values bonds: 0.871936 angles: 0.770757 torsions: N/A planes: 1.60444 non-bonded: 0.000174849 chiral vol: 0.946607 rama plot: -176.918 start_pos: N/A Minimum found (iteration number 280) at -1266.3 Final Estimated RMS Z Scores: bonds: 0.215667 angles: 0.524248 torsions: N/A planes: 1.5292 non-bonded: 0.000237911 chiral vol: 0.434753 rama plot: -178.371 start_pos: N/A SUCCESS TIME:: (dragged refinement): 74.966 Refinement elapsed time: 0.041 INFO:: replace_coords: 22 atoms updated. centering on A 59 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 5 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 58 and 60 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -522.921 Initial RMS Z values bonds: 0.479261 angles: 0.513599 torsions: N/A planes: 0.871453 non-bonded: 1.99583 chiral vol: 0.464891 rama plot: -174.222 start_pos: N/A Minimum found (iteration number 2) at -1082.16 Final Estimated RMS Z Scores: bonds: 1.57157 angles: 1.13393 torsions: N/A planes: 0.829797 non-bonded: 0.0964135 chiral vol: 0.293532 rama plot: -181.98 start_pos: N/A SUCCESS TIME:: (dragged refinement): 75.576 Refinement elapsed time: 0.058 INFO:: replace_coords: 22 atoms updated. centering on A 60 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 59 and 61 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -870.041 Initial RMS Z values bonds: 1.79285 angles: 1.2652 torsions: N/A planes: 0.672696 non-bonded: 0.146514 chiral vol: 0.36285 rama plot: -158.483 start_pos: N/A Minimum found (iteration number 328) at -903.349 Final Estimated RMS Z Scores: bonds: 1.71502 angles: 1.26188 torsions: N/A planes: 0.821486 non-bonded: 0.144034 chiral vol: 0.366106 rama plot: -169.442 start_pos: N/A SUCCESS TIME:: (dragged refinement): 76.141 Refinement elapsed time: 0.043 INFO:: replace_coords: 18 atoms updated. centering on A 61 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 60 and 62 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -861.998 Initial RMS Z values bonds: 1.96784 angles: 1.38971 torsions: N/A planes: 1.08063 non-bonded: 0 chiral vol: 0.694237 rama plot: -170.548 start_pos: N/A Minimum found (iteration number 291) at -982.502 Final Estimated RMS Z Scores: bonds: 0.131321 angles: 0.519236 torsions: N/A planes: 0.915165 non-bonded: 0 chiral vol: 0.223736 rama plot: -169.788 start_pos: N/A SUCCESS TIME:: (dragged refinement): 76.74 Refinement elapsed time: 0.035 INFO:: replace_coords: 16 atoms updated. centering on A 62 CA created 17 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 61 and 63 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1096.83 Initial RMS Z values bonds: 0.655043 angles: 0.781614 torsions: N/A planes: 1.01329 non-bonded: 0 chiral vol: 0.420624 rama plot: -172.225 start_pos: N/A Minimum found (iteration number 308) at -1144.07 Final Estimated RMS Z Scores: bonds: 0.134565 angles: 0.312675 torsions: N/A planes: 1.15451 non-bonded: 0 chiral vol: 0.339649 rama plot: -182.959 start_pos: N/A SUCCESS TIME:: (dragged refinement): 77.355 Refinement elapsed time: 0.043 INFO:: replace_coords: 20 atoms updated. centering on A 63 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 62 and 64 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1201.79 Initial RMS Z values bonds: 0.449177 angles: 0.567967 torsions: N/A planes: 1.18871 non-bonded: 0 chiral vol: 0.308153 rama plot: -175.017 start_pos: N/A Minimum found (iteration number 302) at -1234 Final Estimated RMS Z Scores: bonds: 0.143474 angles: 0.371398 torsions: N/A planes: 0.880094 non-bonded: 0 chiral vol: 0.186418 rama plot: -181.431 start_pos: N/A SUCCESS TIME:: (dragged refinement): 77.983 Refinement elapsed time: 0.048 INFO:: replace_coords: 23 atoms updated. centering on A 64 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 63 and 65 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1298.4 Initial RMS Z values bonds: 0.62506 angles: 0.537976 torsions: N/A planes: 1.09993 non-bonded: 0 chiral vol: 0.238162 rama plot: -175.165 start_pos: N/A Minimum found (iteration number 64) at -1345.72 Final Estimated RMS Z Scores: bonds: 0.143094 angles: 0.315076 torsions: N/A planes: 0.795181 non-bonded: 0 chiral vol: 0.293496 rama plot: -186.561 start_pos: N/A SUCCESS TIME:: (dragged refinement): 78.645 Refinement elapsed time: 0.085 INFO:: replace_coords: 29 atoms updated. centering on A 65 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 64 and 66 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1043.29 Initial RMS Z values bonds: 0.408818 angles: 0.365867 torsions: N/A planes: 1.19092 non-bonded: 0 chiral vol: 0.337163 rama plot: -151.551 start_pos: N/A Minimum found (iteration number 2) at -1058.23 Final Estimated RMS Z Scores: bonds: 0.130421 angles: 0.371262 torsions: N/A planes: 0.89457 non-bonded: 0 chiral vol: 0.378763 rama plot: -155.225 start_pos: N/A SUCCESS TIME:: (dragged refinement): 79.31 Refinement elapsed time: 0.062 INFO:: replace_coords: 22 atoms updated. centering on A 66 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 65 and 67 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1036.02 Initial RMS Z values bonds: 0.672405 angles: 0.811569 torsions: N/A planes: 1.25893 non-bonded: 0 chiral vol: 0.611605 rama plot: -156.636 start_pos: N/A Minimum found (iteration number 331) at -1080.77 Final Estimated RMS Z Scores: bonds: 0.156644 angles: 0.532483 torsions: N/A planes: 1.09342 non-bonded: 0 chiral vol: 0.42452 rama plot: -163.912 start_pos: N/A SUCCESS TIME:: (dragged refinement): 79.969 Refinement elapsed time: 0.048 INFO:: replace_coords: 22 atoms updated. centering on A 67 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 66 and 68 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1120.85 Initial RMS Z values bonds: 0.655926 angles: 0.689415 torsions: N/A planes: 1.18426 non-bonded: 0 chiral vol: 0.460334 rama plot: -156.205 start_pos: N/A unexpected error from gsl_multimin_fdfminimizer_iterate Error in gsl_multimin_fdfminimizer_iterate was GSL_ENOPROG Final Estimated RMS Z Scores bonds: 0.158159 angles: 0.485353 torsions: N/A planes: 0.955971 non-bonded: 0 chiral vol: 0.373837 rama plot: -155.839 start_pos: N/A NOPROGRESS TIME:: (dragged refinement): 80.613 Refinement elapsed time: 0.019 INFO:: replace_coords: 22 atoms updated. centering on A 68 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 67 and 69 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1425.28 Initial RMS Z values bonds: 0.684789 angles: 0.62776 torsions: N/A planes: 1.48192 non-bonded: 0 chiral vol: 0.747244 rama plot: -172.348 start_pos: N/A Minimum found (iteration number 321) at -1462.23 Final Estimated RMS Z Scores: bonds: 0.117212 angles: 0.40519 torsions: N/A planes: 1.17814 non-bonded: 0 chiral vol: 0.324229 rama plot: -174.1 start_pos: N/A SUCCESS TIME:: (dragged refinement): 81.33 Refinement elapsed time: 0.061 INFO:: replace_coords: 29 atoms updated. centering on A 69 CA created 27 bond restraints created 30 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 68 and 70 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1507.83 Initial RMS Z values bonds: 0.715093 angles: 0.589273 torsions: N/A planes: 1.19869 non-bonded: 0.0195401 chiral vol: 0.374731 rama plot: -178.482 start_pos: N/A Minimum found (iteration number 378) at -1540.39 Final Estimated RMS Z Scores: bonds: 0.202302 angles: 0.370179 torsions: N/A planes: 1.14084 non-bonded: 0.000192847 chiral vol: 0.182046 rama plot: -179.195 start_pos: N/A SUCCESS TIME:: (dragged refinement): 82.101 Refinement elapsed time: 0.068 INFO:: replace_coords: 30 atoms updated. centering on A 70 CA created 24 bond restraints created 27 angle restraints created 1 plane restraints created 5 chiral vol restraints created 57 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 69 and 71 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 3 plane links initial distortion_score: -1268.86 Initial RMS Z values bonds: 0.791771 angles: 0.67537 torsions: N/A planes: 1.1112 non-bonded: 0.000199245 chiral vol: 0.321495 rama plot: -178.879 start_pos: N/A Minimum found (iteration number 344) at -1297.72 Final Estimated RMS Z Scores: bonds: 0.162176 angles: 0.382022 torsions: N/A planes: 1.06682 non-bonded: 0.000166942 chiral vol: 0.198 rama plot: -178.596 start_pos: N/A SUCCESS TIME:: (dragged refinement): 82.949 Refinement elapsed time: 0.054 INFO:: replace_coords: 27 atoms updated. centering on A 71 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 4 chiral vol restraints created 39 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 70 and 72 of chain A Link restraints: 1 bond links 3 angle links 3 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 160.557 Initial RMS Z values bonds: 0.437762 angles: 0.615971 torsions: N/A planes: 2.08176 non-bonded: 3.77293 chiral vol: 0.218343 rama plot: -183.125 start_pos: N/A Minimum found (iteration number 292) at -840.954 Final Estimated RMS Z Scores: bonds: 0.321178 angles: 0.550897 torsions: N/A planes: 2.45641 non-bonded: 0.00186759 chiral vol: 0.231848 rama plot: -182.942 start_pos: N/A SUCCESS TIME:: (dragged refinement): 83.782 Refinement elapsed time: 0.038 INFO:: replace_coords: 20 atoms updated. centering on A 72 CA created 13 bond restraints created 12 angle restraints created 0 plane restraints created 2 chiral vol restraints created 27 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 71 and 73 of chain A Link restraints: 1 bond links 3 angle links 3 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -699.992 Initial RMS Z values bonds: 0.48151 angles: 0.646482 torsions: N/A planes: 2.30277 non-bonded: 0.00277186 chiral vol: 0.240258 rama plot: -155.036 start_pos: N/A Minimum found (iteration number 348) at -739.211 Final Estimated RMS Z Scores: bonds: 0.234702 angles: 0.912423 torsions: N/A planes: 1.20236 non-bonded: 0.00101037 chiral vol: 0.213919 rama plot: -173.85 start_pos: N/A SUCCESS TIME:: (dragged refinement): 84.585 Refinement elapsed time: 0.036 INFO:: replace_coords: 16 atoms updated. centering on A 73 CA created 14 bond restraints created 13 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 72 and 74 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 3 plane links initial distortion_score: -894.95 Initial RMS Z values bonds: 0.982242 angles: 1.12257 torsions: N/A planes: 1.27175 non-bonded: 2.37013e-05 chiral vol: 0.233598 rama plot: -187.371 start_pos: N/A Minimum found (iteration number 121) at -957.195 Final Estimated RMS Z Scores: bonds: 0.166215 angles: 0.334861 torsions: N/A planes: 0.598794 non-bonded: 0 chiral vol: 0.500751 rama plot: -196.51 start_pos: N/A SUCCESS TIME:: (dragged refinement): 85.372 Refinement elapsed time: 0.058 INFO:: replace_coords: 17 atoms updated. centering on A 74 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 73 and 75 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1160.07 Initial RMS Z values bonds: 0.347372 angles: 0.54121 torsions: N/A planes: 0.605638 non-bonded: 0 chiral vol: 0.570274 rama plot: -188.591 start_pos: N/A Minimum found (iteration number 269) at -1174.37 Final Estimated RMS Z Scores: bonds: 0.157313 angles: 0.323667 torsions: N/A planes: 0.545157 non-bonded: 0 chiral vol: 0.378576 rama plot: -191.213 start_pos: N/A SUCCESS TIME:: (dragged refinement): 86.05 Refinement elapsed time: 0.036 INFO:: replace_coords: 18 atoms updated. centering on A 75 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 74 and 76 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1212.39 Initial RMS Z values bonds: 0.421286 angles: 1.11608 torsions: N/A planes: 0.686084 non-bonded: 0 chiral vol: 0.72101 rama plot: -188.552 start_pos: N/A Minimum found (iteration number 310) at -1263.77 Final Estimated RMS Z Scores: bonds: 0.151531 angles: 0.306859 torsions: N/A planes: 0.525283 non-bonded: 0 chiral vol: 0.313821 rama plot: -192.618 start_pos: N/A SUCCESS TIME:: (dragged refinement): 86.768 Refinement elapsed time: 0.044 INFO:: replace_coords: 21 atoms updated. centering on A 76 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 75 and 77 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1166.04 Initial RMS Z values bonds: 0.749051 angles: 0.715978 torsions: N/A planes: 0.466839 non-bonded: 0 chiral vol: 0.218504 rama plot: -166.295 start_pos: N/A Minimum found (iteration number 72) at -1198 Final Estimated RMS Z Scores: bonds: 0.146403 angles: 0.430328 torsions: N/A planes: 0.562341 non-bonded: 0 chiral vol: 0.327502 rama plot: -169.954 start_pos: N/A SUCCESS TIME:: (dragged refinement): 87.551 Refinement elapsed time: 0.069 INFO:: replace_coords: 21 atoms updated. centering on A 77 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 76 and 78 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1336.17 Initial RMS Z values bonds: 0.938023 angles: 0.724883 torsions: N/A planes: 0.665344 non-bonded: 0 chiral vol: 0.355821 rama plot: -160.891 start_pos: N/A Minimum found (iteration number 331) at -1375.91 Final Estimated RMS Z Scores: bonds: 0.172127 angles: 0.470987 torsions: N/A planes: 0.516149 non-bonded: 0 chiral vol: 0.349842 rama plot: -163.684 start_pos: N/A SUCCESS TIME:: (dragged refinement): 88.382 Refinement elapsed time: 0.057 INFO:: replace_coords: 25 atoms updated. centering on A 78 CA created 23 bond restraints created 26 angle restraints created 3 plane restraints created 3 chiral vol restraints created 55 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 77 and 79 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1437.93 Initial RMS Z values bonds: 0.58949 angles: 0.826661 torsions: N/A planes: 1.0233 non-bonded: 0 chiral vol: 1.08929 rama plot: -158.843 start_pos: N/A Minimum found (iteration number 2) at -1484.79 Final Estimated RMS Z Scores: bonds: 0.145435 angles: 0.393601 torsions: N/A planes: 0.557115 non-bonded: 0 chiral vol: 0.294519 rama plot: -160.806 start_pos: N/A SUCCESS TIME:: (dragged refinement): 89.213 Refinement elapsed time: 0.072 INFO:: replace_coords: 26 atoms updated. centering on A 79 CA created 27 bond restraints created 32 angle restraints created 3 plane restraints created 3 chiral vol restraints created 65 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 78 and 80 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1622.06 Initial RMS Z values bonds: 1.06925 angles: 0.742856 torsions: N/A planes: 0.835185 non-bonded: 0 chiral vol: 1.02444 rama plot: -168.289 start_pos: N/A Minimum found (iteration number 268) at -1690.22 Final Estimated RMS Z Scores: bonds: 0.147166 angles: 0.294621 torsions: N/A planes: 0.323116 non-bonded: 0 chiral vol: 0.131287 rama plot: -168.717 start_pos: N/A SUCCESS TIME:: (dragged refinement): 90.082 Refinement elapsed time: 0.055 INFO:: replace_coords: 29 atoms updated. centering on A 80 CA created 31 bond restraints created 38 angle restraints created 3 plane restraints created 3 chiral vol restraints created 75 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 79 and 81 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1655.69 Initial RMS Z values bonds: 0.905513 angles: 0.590352 torsions: N/A planes: 1.53767 non-bonded: 0 chiral vol: 0.714792 rama plot: -176.381 start_pos: N/A Minimum found (iteration number 306) at -1724.78 Final Estimated RMS Z Scores: bonds: 0.199105 angles: 0.210919 torsions: N/A planes: 0.820464 non-bonded: 0 chiral vol: 0.137994 rama plot: -179.517 start_pos: N/A SUCCESS TIME:: (dragged refinement): 90.923 Refinement elapsed time: 0.062 INFO:: replace_coords: 32 atoms updated. centering on A 81 CA created 30 bond restraints created 37 angle restraints created 2 plane restraints created 4 chiral vol restraints created 73 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 80 and 82 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1603.45 Initial RMS Z values bonds: 0.554008 angles: 0.795847 torsions: N/A planes: 0.912734 non-bonded: 0 chiral vol: 0.901175 rama plot: -181.019 start_pos: N/A Minimum found (iteration number 227) at -1644.52 Final Estimated RMS Z Scores: bonds: 0.133399 angles: 0.214799 torsions: N/A planes: 0.851648 non-bonded: 0 chiral vol: 0.126573 rama plot: -180.917 start_pos: N/A SUCCESS TIME:: (dragged refinement): 91.727 Refinement elapsed time: 0.047 INFO:: replace_coords: 31 atoms updated. centering on A 82 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 81 and 83 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1341.51 Initial RMS Z values bonds: 0.304517 angles: 0.318103 torsions: N/A planes: 1.17883 non-bonded: 0 chiral vol: 0.143387 rama plot: -178.034 start_pos: N/A Minimum found (iteration number 230) at -1350.41 Final Estimated RMS Z Scores: bonds: 0.124652 angles: 0.208355 torsions: N/A planes: 0.960723 non-bonded: 0 chiral vol: 0.112108 rama plot: -178.058 start_pos: N/A SUCCESS TIME:: (dragged refinement): 92.445 Refinement elapsed time: 0.039 INFO:: replace_coords: 23 atoms updated. centering on A 83 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 82 and 84 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1179.41 Initial RMS Z values bonds: 0.593701 angles: 0.748717 torsions: N/A planes: 0.987863 non-bonded: 0 chiral vol: 0.367853 rama plot: -161.287 start_pos: N/A Minimum found (iteration number 211) at -1207.4 Final Estimated RMS Z Scores: bonds: 0.158852 angles: 0.422231 torsions: N/A planes: 0.87568 non-bonded: 0 chiral vol: 0.657888 rama plot: -165.866 start_pos: N/A SUCCESS TIME:: (dragged refinement): 93.097 Refinement elapsed time: 0.03 INFO:: replace_coords: 19 atoms updated. centering on A 84 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 2 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 83 and 85 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1120.42 Initial RMS Z values bonds: 0.322788 angles: 0.546215 torsions: N/A planes: 0.957928 non-bonded: 0.00329346 chiral vol: 0.824601 rama plot: -146.657 start_pos: N/A Minimum found (iteration number 154) at -1146.96 Final Estimated RMS Z Scores: bonds: 0.182433 angles: 0.467813 torsions: N/A planes: 0.76463 non-bonded: 0 chiral vol: 0.91975 rama plot: -152.639 start_pos: N/A SUCCESS TIME:: (dragged refinement): 93.78 Refinement elapsed time: 0.081 INFO:: replace_coords: 22 atoms updated. centering on A 85 CA created 29 bond restraints created 35 angle restraints created 3 plane restraints created 3 chiral vol restraints created 70 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 84 and 86 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1308.78 Initial RMS Z values bonds: 0.52238 angles: 0.609773 torsions: N/A planes: 0.846826 non-bonded: 0 chiral vol: 0.76818 rama plot: -147.364 start_pos: N/A Minimum found (iteration number 98) at -1325.87 Final Estimated RMS Z Scores: bonds: 0.159119 angles: 0.477205 torsions: N/A planes: 0.80566 non-bonded: 0 chiral vol: 0.793041 rama plot: -147.503 start_pos: N/A SUCCESS TIME:: (dragged refinement): 94.555 Refinement elapsed time: 0.103 INFO:: replace_coords: 30 atoms updated. centering on A 86 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 85 and 87 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1212.98 Initial RMS Z values bonds: 0.410242 angles: 0.549513 torsions: N/A planes: 0.917103 non-bonded: 0.000329187 chiral vol: 0.536432 rama plot: -164.386 start_pos: N/A Minimum found (iteration number 68) at -1251.35 Final Estimated RMS Z Scores: bonds: 0.156173 angles: 0.427569 torsions: N/A planes: 0.796924 non-bonded: 0 chiral vol: 0.546398 rama plot: -176.139 start_pos: N/A SUCCESS TIME:: (dragged refinement): 95.299 Refinement elapsed time: 0.085 INFO:: replace_coords: 27 atoms updated. centering on A 87 CA created 22 bond restraints created 26 angle restraints created 1 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 86 and 88 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1200.52 Initial RMS Z values bonds: 0.570611 angles: 0.889658 torsions: N/A planes: 0.905568 non-bonded: 0 chiral vol: 0.592851 rama plot: -183.308 start_pos: N/A Minimum found (iteration number 291) at -1229.06 Final Estimated RMS Z Scores: bonds: 0.161591 angles: 0.645824 torsions: N/A planes: 0.728967 non-bonded: 0 chiral vol: 0.427723 rama plot: -183.358 start_pos: N/A SUCCESS TIME:: (dragged refinement): 95.937 Refinement elapsed time: 0.044 INFO:: replace_coords: 24 atoms updated. centering on A 88 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 87 and 89 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 35.4778 Initial RMS Z values bonds: 1.39581 angles: 1.15039 torsions: N/A planes: 1.79321 non-bonded: 2.81868 chiral vol: 0.628006 rama plot: -180.274 start_pos: N/A Minimum found (iteration number 392) at -1097.14 Final Estimated RMS Z Scores: bonds: 0.105278 angles: 0.425344 torsions: N/A planes: 0.491709 non-bonded: 0.000224361 chiral vol: 0.151372 rama plot: -190.619 start_pos: N/A SUCCESS TIME:: (dragged refinement): 96.725 Refinement elapsed time: 0.232 INFO:: replace_coords: 23 atoms updated. centering on A 89 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 4 chiral vol restraints created 52 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 88 and 90 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1129.73 Initial RMS Z values bonds: 0.272672 angles: 0.824406 torsions: N/A planes: 0.550889 non-bonded: 0.000189844 chiral vol: 0.562061 rama plot: -177.163 start_pos: N/A Minimum found (iteration number 197) at -1152.46 Final Estimated RMS Z Scores: bonds: 0.139104 angles: 0.488074 torsions: N/A planes: 0.601271 non-bonded: 0.000234915 chiral vol: 0.313385 rama plot: -177.915 start_pos: N/A SUCCESS TIME:: (dragged refinement): 97.508 Refinement elapsed time: 0.155 INFO:: replace_coords: 24 atoms updated. centering on A 90 CA created 23 bond restraints created 26 angle restraints created 1 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 89 and 91 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1128.63 Initial RMS Z values bonds: 0.660651 angles: 1.06933 torsions: N/A planes: 0.870522 non-bonded: 0.0287831 chiral vol: 0.832959 rama plot: -178.389 start_pos: N/A Minimum found (iteration number 307) at -1190.14 Final Estimated RMS Z Scores: bonds: 0.14956 angles: 0.393758 torsions: N/A planes: 0.716798 non-bonded: 0.000197565 chiral vol: 0.4674 rama plot: -179.299 start_pos: N/A SUCCESS TIME:: (dragged refinement): 98.258 Refinement elapsed time: 0.114 INFO:: replace_coords: 25 atoms updated. centering on A 91 CA created 19 bond restraints created 21 angle restraints created 0 plane restraints created 4 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 90 and 92 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1218.42 Initial RMS Z values bonds: 1.63294 angles: 0.608776 torsions: N/A planes: 0.805874 non-bonded: 0 chiral vol: 0.388396 rama plot: -178.385 start_pos: N/A Minimum found (iteration number 364) at -1288.78 Final Estimated RMS Z Scores: bonds: 0.141602 angles: 0.488095 torsions: N/A planes: 0.799399 non-bonded: 2.26638e-07 chiral vol: 0.380622 rama plot: -179.78 start_pos: N/A SUCCESS TIME:: (dragged refinement): 99.022 Refinement elapsed time: 0.052 INFO:: replace_coords: 22 atoms updated. centering on A 92 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 91 and 93 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -1010.21 Initial RMS Z values bonds: 0.839156 angles: 1.04734 torsions: N/A planes: 0.786557 non-bonded: 0.000466942 chiral vol: 0.7159 rama plot: -176.737 start_pos: N/A Minimum found (iteration number 2) at -1065.11 Final Estimated RMS Z Scores: bonds: 0.117969 angles: 0.295733 torsions: N/A planes: 0.442467 non-bonded: 0 chiral vol: 0.262916 rama plot: -174.595 start_pos: N/A SUCCESS TIME:: (dragged refinement): 99.849 Refinement elapsed time: 0.058 INFO:: replace_coords: 24 atoms updated. centering on A 93 CA created 14 bond restraints created 16 angle restraints created 1 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 92 and 93 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -648.659 Initial RMS Z values bonds: 0.0926447 angles: 0.129567 torsions: N/A planes: 0.125162 non-bonded: 0 chiral vol: 0.0745397 rama plot: N/A start_pos: N/A Minimum found (iteration number 126) at -648.87 Final Estimated RMS Z Scores: bonds: 0.088792 angles: 0.108995 torsions: N/A planes: 0.175442 non-bonded: 0 chiral vol: 0.0429001 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 100.585 Refinement elapsed time: 0.014 INFO:: replace_coords: 16 atoms updated. There are 96 residues in chain B centering on B 1 CA created 13 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain B Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -322.213 Initial RMS Z values bonds: 1.12652 angles: 1.22618 torsions: N/A planes: 1.45687 non-bonded: 0 chiral vol: 1.12007 rama plot: N/A start_pos: N/A Minimum found (iteration number 299) at -367.413 Final Estimated RMS Z Scores: bonds: 0.117591 angles: 0.516761 torsions: N/A planes: 1.47555 non-bonded: 0 chiral vol: 0.379689 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 101.162 Refinement elapsed time: 0.025 INFO:: replace_coords: 15 atoms updated. centering on B 2 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 1 and 3 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -665.6 Initial RMS Z values bonds: 0.619915 angles: 0.726464 torsions: N/A planes: 1.26613 non-bonded: 0 chiral vol: 0.310295 rama plot: -175.627 start_pos: N/A Minimum found (iteration number 91) at -688.347 Final Estimated RMS Z Scores: bonds: 0.146301 angles: 0.344113 torsions: N/A planes: 1.01931 non-bonded: 0 chiral vol: 0.3227 rama plot: -179.682 start_pos: N/A SUCCESS TIME:: (dragged refinement): 101.831 Refinement elapsed time: 0.059 INFO:: replace_coords: 21 atoms updated. centering on B 3 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 2 and 4 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -879.622 Initial RMS Z values bonds: 0.290087 angles: 0.529655 torsions: N/A planes: 0.970864 non-bonded: 0 chiral vol: 0.365257 rama plot: -155.117 start_pos: N/A Minimum found (iteration number 314) at -912.623 Final Estimated RMS Z Scores: bonds: 0.22038 angles: 0.471036 torsions: N/A planes: 1.08904 non-bonded: 0 chiral vol: 0.374986 rama plot: -170.866 start_pos: N/A SUCCESS TIME:: (dragged refinement): 102.475 Refinement elapsed time: 0.038 INFO:: replace_coords: 17 atoms updated. centering on B 4 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 3 and 5 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -880.597 Initial RMS Z values bonds: 0.606515 angles: 1.0196 torsions: N/A planes: 1.01921 non-bonded: 0 chiral vol: 1.05716 rama plot: -167.389 start_pos: N/A Minimum found (iteration number 319) at -920.643 Final Estimated RMS Z Scores: bonds: 0.185859 angles: 0.363409 torsions: N/A planes: 0.691409 non-bonded: 0 chiral vol: 0.278341 rama plot: -169.197 start_pos: N/A SUCCESS TIME:: (dragged refinement): 103.14 Refinement elapsed time: 0.037 INFO:: replace_coords: 17 atoms updated. centering on B 5 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 4 and 6 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -903.835 Initial RMS Z values bonds: 1.15772 angles: 0.621842 torsions: N/A planes: 0.878408 non-bonded: 0 chiral vol: 0.232885 rama plot: -156.007 start_pos: N/A Minimum found (iteration number 305) at -940.313 Final Estimated RMS Z Scores: bonds: 0.160096 angles: 0.313227 torsions: N/A planes: 0.685414 non-bonded: 0 chiral vol: 0.158443 rama plot: -156.704 start_pos: N/A SUCCESS TIME:: (dragged refinement): 103.792 Refinement elapsed time: 0.037 INFO:: replace_coords: 18 atoms updated. centering on B 6 CA created 17 bond restraints created 19 angle restraints created 0 plane restraints created 4 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 5 and 7 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1230.35 Initial RMS Z values bonds: 0.757477 angles: 0.427642 torsions: N/A planes: 0.955664 non-bonded: 0 chiral vol: 0.397825 rama plot: -180.464 start_pos: N/A Minimum found (iteration number 291) at -1251.86 Final Estimated RMS Z Scores: bonds: 0.179032 angles: 0.279187 torsions: N/A planes: 0.558363 non-bonded: 0 chiral vol: 0.158141 rama plot: -181.453 start_pos: N/A SUCCESS TIME:: (dragged refinement): 104.493 Refinement elapsed time: 0.039 INFO:: replace_coords: 20 atoms updated. centering on B 7 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 6 and 8 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1334.72 Initial RMS Z values bonds: 0.959923 angles: 0.55613 torsions: N/A planes: 0.466977 non-bonded: 0 chiral vol: 0.463042 rama plot: -191.769 start_pos: N/A Minimum found (iteration number 266) at -1370.16 Final Estimated RMS Z Scores: bonds: 0.212076 angles: 0.324099 torsions: N/A planes: 0.469128 non-bonded: 0 chiral vol: 0.229176 rama plot: -195.159 start_pos: N/A SUCCESS TIME:: (dragged refinement): 105.151 Refinement elapsed time: 0.037 INFO:: replace_coords: 21 atoms updated. centering on B 8 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 3 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 7 and 9 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1380.22 Initial RMS Z values bonds: 0.644507 angles: 0.639134 torsions: N/A planes: 0.556816 non-bonded: 0 chiral vol: 0.362128 rama plot: -196.363 start_pos: N/A Minimum found (iteration number 299) at -1411.53 Final Estimated RMS Z Scores: bonds: 0.147321 angles: 0.29457 torsions: N/A planes: 0.525406 non-bonded: 0 chiral vol: 0.15507 rama plot: -202.704 start_pos: N/A SUCCESS TIME:: (dragged refinement): 105.786 Refinement elapsed time: 0.04 INFO:: replace_coords: 20 atoms updated. centering on B 9 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 8 and 10 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1198.1 Initial RMS Z values bonds: 0.572477 angles: 0.37194 torsions: N/A planes: 0.658702 non-bonded: 0 chiral vol: 0.318752 rama plot: -201.309 start_pos: N/A Minimum found (iteration number 343) at -1218.98 Final Estimated RMS Z Scores: bonds: 0.200663 angles: 0.396277 torsions: N/A planes: 1.04865 non-bonded: 0 chiral vol: 0.357256 rama plot: -212.055 start_pos: N/A SUCCESS TIME:: (dragged refinement): 106.381 Refinement elapsed time: 0.046 INFO:: replace_coords: 19 atoms updated. centering on B 10 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 9 and 11 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1149.32 Initial RMS Z values bonds: 0.913168 angles: 0.754257 torsions: N/A planes: 1.33136 non-bonded: 0 chiral vol: 0.632512 rama plot: -195.815 start_pos: N/A Minimum found (iteration number 325) at -1202.48 Final Estimated RMS Z Scores: bonds: 0.222733 angles: 0.498389 torsions: N/A planes: 0.785143 non-bonded: 0 chiral vol: 0.325551 rama plot: -205.423 start_pos: N/A SUCCESS TIME:: (dragged refinement): 107.043 Refinement elapsed time: 0.043 INFO:: replace_coords: 19 atoms updated. centering on B 11 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 10 and 12 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -522.332 Initial RMS Z values bonds: 1.21524 angles: 0.892766 torsions: N/A planes: 0.969703 non-bonded: 2.13489 chiral vol: 0.443016 rama plot: -184.932 start_pos: N/A Minimum found (iteration number 370) at -1043.25 Final Estimated RMS Z Scores: bonds: 1.65493 angles: 1.2102 torsions: N/A planes: 0.994567 non-bonded: 0.118526 chiral vol: 0.367104 rama plot: -191.295 start_pos: N/A SUCCESS TIME:: (dragged refinement): 107.733 Refinement elapsed time: 0.054 INFO:: replace_coords: 20 atoms updated. centering on B 12 CA created 21 bond restraints created 24 angle restraints created 0 plane restraints created 3 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 11 and 13 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -565.346 Initial RMS Z values bonds: 1.63892 angles: 1.15767 torsions: N/A planes: 0.994588 non-bonded: 1.79418 chiral vol: 0.327061 rama plot: -180.997 start_pos: N/A Minimum found (iteration number 54) at -984.878 Final Estimated RMS Z Scores: bonds: 2.15085 angles: 1.56577 torsions: N/A planes: 0.998602 non-bonded: 0.207105 chiral vol: 0.343655 rama plot: -185.491 start_pos: N/A SUCCESS TIME:: (dragged refinement): 108.437 Refinement elapsed time: 0.066 INFO:: replace_coords: 22 atoms updated. centering on B 13 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 3 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 12 and 14 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1079.07 Initial RMS Z values bonds: 2.14919 angles: 1.61366 torsions: N/A planes: 0.975428 non-bonded: 0.0831798 chiral vol: 0.254543 rama plot: -188.603 start_pos: N/A Minimum found (iteration number 350) at -1214.3 Final Estimated RMS Z Scores: bonds: 1.5105 angles: 1.11393 torsions: N/A planes: 0.867719 non-bonded: 0.0831583 chiral vol: 0.227162 rama plot: -196.075 start_pos: N/A SUCCESS TIME:: (dragged refinement): 109.088 Refinement elapsed time: 0.056 INFO:: replace_coords: 23 atoms updated. centering on B 14 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 13 and 15 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1237.42 Initial RMS Z values bonds: 1.70314 angles: 1.16702 torsions: N/A planes: 0.878558 non-bonded: 0 chiral vol: 0.215493 rama plot: -204.246 start_pos: N/A Minimum found (iteration number 64) at -1370.26 Final Estimated RMS Z Scores: bonds: 0.15755 angles: 0.394701 torsions: N/A planes: 0.866651 non-bonded: 0 chiral vol: 0.0919183 rama plot: -211.074 start_pos: N/A SUCCESS TIME:: (dragged refinement): 109.776 Refinement elapsed time: 0.065 INFO:: replace_coords: 21 atoms updated. centering on B 15 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 14 and 16 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1363.41 Initial RMS Z values bonds: 0.300554 angles: 0.813369 torsions: N/A planes: 0.811786 non-bonded: 0 chiral vol: 0.559188 rama plot: -215.067 start_pos: N/A Minimum found (iteration number 257) at -1389.25 Final Estimated RMS Z Scores: bonds: 0.138084 angles: 0.290828 torsions: N/A planes: 0.60282 non-bonded: 4.22116e-06 chiral vol: 0.160996 rama plot: -216.614 start_pos: N/A SUCCESS TIME:: (dragged refinement): 110.442 Refinement elapsed time: 0.037 INFO:: replace_coords: 21 atoms updated. centering on B 16 CA created 17 bond restraints created 19 angle restraints created 1 plane restraints created 4 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 15 and 17 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1330.03 Initial RMS Z values bonds: 0.764853 angles: 0.850763 torsions: N/A planes: 0.677968 non-bonded: 3.95734e-06 chiral vol: 0.678371 rama plot: -220.349 start_pos: N/A Minimum found (iteration number 313) at -1360.27 Final Estimated RMS Z Scores: bonds: 0.227733 angles: 0.418217 torsions: N/A planes: 0.53737 non-bonded: 0 chiral vol: 0.334183 rama plot: -221.096 start_pos: N/A SUCCESS TIME:: (dragged refinement): 111.027 Refinement elapsed time: 0.041 INFO:: replace_coords: 20 atoms updated. centering on B 17 CA created 19 bond restraints created 22 angle restraints created 1 plane restraints created 5 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 16 and 18 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1400.74 Initial RMS Z values bonds: 0.824056 angles: 0.622055 torsions: N/A planes: 0.591687 non-bonded: 0 chiral vol: 0.549434 rama plot: -217.752 start_pos: N/A Minimum found (iteration number 289) at -1435.09 Final Estimated RMS Z Scores: bonds: 0.171691 angles: 0.404245 torsions: N/A planes: 0.454864 non-bonded: 0 chiral vol: 0.274022 rama plot: -220.46 start_pos: N/A SUCCESS TIME:: (dragged refinement): 111.605 Refinement elapsed time: 0.044 INFO:: replace_coords: 22 atoms updated. centering on B 18 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 17 and 19 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1399.05 Initial RMS Z values bonds: 0.603711 angles: 0.522516 torsions: N/A planes: 0.431951 non-bonded: 0 chiral vol: 0.440786 rama plot: -218.317 start_pos: N/A Minimum found (iteration number 355) at -1423.07 Final Estimated RMS Z Scores: bonds: 0.132407 angles: 0.31449 torsions: N/A planes: 0.250673 non-bonded: 0 chiral vol: 0.25916 rama plot: -220.84 start_pos: N/A SUCCESS TIME:: (dragged refinement): 112.257 Refinement elapsed time: 0.054 INFO:: replace_coords: 23 atoms updated. centering on B 19 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 18 and 20 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1356.67 Initial RMS Z values bonds: 0.428709 angles: 0.527033 torsions: N/A planes: 0.530936 non-bonded: 0 chiral vol: 0.34184 rama plot: -219.236 start_pos: N/A Minimum found (iteration number 349) at -1372.02 Final Estimated RMS Z Scores: bonds: 0.142518 angles: 0.373121 torsions: N/A planes: 0.432519 non-bonded: 0 chiral vol: 0.236702 rama plot: -221.347 start_pos: N/A SUCCESS TIME:: (dragged refinement): 112.855 Refinement elapsed time: 0.054 INFO:: replace_coords: 23 atoms updated. centering on B 20 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 19 and 21 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1291.03 Initial RMS Z values bonds: 0.695438 angles: 0.646012 torsions: N/A planes: 0.43725 non-bonded: 0 chiral vol: 0.342672 rama plot: -219.733 start_pos: N/A Minimum found (iteration number 347) at -1322.64 Final Estimated RMS Z Scores: bonds: 0.100515 angles: 0.222642 torsions: N/A planes: 0.346295 non-bonded: 0 chiral vol: 0.189207 rama plot: -221.394 start_pos: N/A SUCCESS TIME:: (dragged refinement): 113.393 Refinement elapsed time: 0.054 INFO:: replace_coords: 24 atoms updated. centering on B 21 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 20 and 22 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1306.58 Initial RMS Z values bonds: 0.524257 angles: 0.392747 torsions: N/A planes: 0.650241 non-bonded: 0 chiral vol: 0.302055 rama plot: -220.343 start_pos: N/A Minimum found (iteration number 287) at -1323.34 Final Estimated RMS Z Scores: bonds: 0.11446 angles: 0.185387 torsions: N/A planes: 0.534081 non-bonded: 0 chiral vol: 0.151341 rama plot: -221.383 start_pos: N/A SUCCESS TIME:: (dragged refinement): 113.976 Refinement elapsed time: 0.046 INFO:: replace_coords: 24 atoms updated. centering on B 22 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 4 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 21 and 23 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1195.31 Initial RMS Z values bonds: 0.459114 angles: 0.600436 torsions: N/A planes: 0.907501 non-bonded: 0 chiral vol: 0.444764 rama plot: -221.356 start_pos: N/A Minimum found (iteration number 285) at -1215.78 Final Estimated RMS Z Scores: bonds: 0.125189 angles: 0.248733 torsions: N/A planes: 0.339036 non-bonded: 1.38299e-06 chiral vol: 0.11851 rama plot: -221.308 start_pos: N/A SUCCESS TIME:: (dragged refinement): 114.563 Refinement elapsed time: 0.04 INFO:: replace_coords: 21 atoms updated. centering on B 23 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 4 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 22 and 24 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1087.88 Initial RMS Z values bonds: 0.40196 angles: 0.513154 torsions: N/A planes: 1.29152 non-bonded: 1.72002e-06 chiral vol: 0.336746 rama plot: -206.651 start_pos: N/A Minimum found (iteration number 341) at -1102.04 Final Estimated RMS Z Scores: bonds: 0.116349 angles: 0.183896 torsions: N/A planes: 0.914318 non-bonded: 1.11239e-06 chiral vol: 0.0699523 rama plot: -206.434 start_pos: N/A SUCCESS TIME:: (dragged refinement): 115.093 Refinement elapsed time: 0.045 INFO:: replace_coords: 19 atoms updated. centering on B 24 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 23 and 25 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -971.306 Initial RMS Z values bonds: 0.656293 angles: 0.584912 torsions: N/A planes: 1.3621 non-bonded: 0 chiral vol: 0.0830469 rama plot: -183.946 start_pos: N/A Minimum found (iteration number 385) at -1001.04 Final Estimated RMS Z Scores: bonds: 0.0919593 angles: 0.276877 torsions: N/A planes: 0.847683 non-bonded: 0 chiral vol: 0.263421 rama plot: -185.845 start_pos: N/A SUCCESS TIME:: (dragged refinement): 115.596 Refinement elapsed time: 0.05 INFO:: replace_coords: 19 atoms updated. centering on B 25 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 24 and 26 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -858.643 Initial RMS Z values bonds: 0.487503 angles: 0.700936 torsions: N/A planes: 0.921533 non-bonded: 0 chiral vol: 0.319215 rama plot: -147.699 start_pos: N/A Minimum found (iteration number 308) at -880.734 Final Estimated RMS Z Scores: bonds: 0.123755 angles: 0.512852 torsions: N/A planes: 0.619254 non-bonded: 0 chiral vol: 0.378419 rama plot: -150.71 start_pos: N/A SUCCESS TIME:: (dragged refinement): 116.168 Refinement elapsed time: 0.04 INFO:: replace_coords: 18 atoms updated. centering on B 26 CA created 17 bond restraints created 18 angle restraints created 1 plane restraints created 2 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 25 and 27 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -119.793 Initial RMS Z values bonds: 1.02543 angles: 0.847897 torsions: N/A planes: 1.34927 non-bonded: 3.4767 chiral vol: 0.379771 rama plot: -152.749 start_pos: N/A Minimum found (iteration number 40) at -765.913 Final Estimated RMS Z Scores: bonds: 1.84864 angles: 1.24482 torsions: N/A planes: 1.04036 non-bonded: 0.164137 chiral vol: 0.390038 rama plot: -151.701 start_pos: N/A SUCCESS TIME:: (dragged refinement): 116.774 Refinement elapsed time: 0.059 INFO:: replace_coords: 19 atoms updated. centering on B 27 CA created 21 bond restraints created 23 angle restraints created 1 plane restraints created 2 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 26 and 28 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -868.184 Initial RMS Z values bonds: 1.9084 angles: 1.31707 torsions: N/A planes: 1.26519 non-bonded: 0.101653 chiral vol: 0.468486 rama plot: -155.145 start_pos: N/A Minimum found (iteration number 391) at -921.066 Final Estimated RMS Z Scores: bonds: 1.69671 angles: 1.12708 torsions: N/A planes: 0.494163 non-bonded: 0.101605 chiral vol: 0.252468 rama plot: -156.983 start_pos: N/A SUCCESS TIME:: (dragged refinement): 117.418 Refinement elapsed time: 0.059 INFO:: replace_coords: 22 atoms updated. centering on B 28 CA created 25 bond restraints created 29 angle restraints created 1 plane restraints created 3 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 27 and 29 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -535.06 Initial RMS Z values bonds: 1.62154 angles: 1.16301 torsions: N/A planes: 1.06596 non-bonded: 1.50699 chiral vol: 0.209267 rama plot: -187.278 start_pos: N/A Minimum found (iteration number 102) at -1138.18 Final Estimated RMS Z Scores: bonds: 1.43956 angles: 1.04964 torsions: N/A planes: 1.06573 non-bonded: 0.0835158 chiral vol: 0.504555 rama plot: -190.742 start_pos: N/A SUCCESS TIME:: (dragged refinement): 118.104 Refinement elapsed time: 0.081 INFO:: replace_coords: 25 atoms updated. centering on B 29 CA created 30 bond restraints created 36 angle restraints created 2 plane restraints created 3 chiral vol restraints created 71 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 28 and 30 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1304.02 Initial RMS Z values bonds: 1.52811 angles: 1.02672 torsions: N/A planes: 1.1844 non-bonded: 0.0626369 chiral vol: 0.633519 rama plot: -186.578 start_pos: N/A Minimum found (iteration number 368) at -1339.48 Final Estimated RMS Z Scores: bonds: 1.34445 angles: 0.970732 torsions: N/A planes: 0.744401 non-bonded: 0.0624851 chiral vol: 0.493406 rama plot: -187.746 start_pos: N/A SUCCESS TIME:: (dragged refinement): 118.841 Refinement elapsed time: 0.072 INFO:: replace_coords: 30 atoms updated. centering on B 30 CA created 24 bond restraints created 28 angle restraints created 1 plane restraints created 3 chiral vol restraints created 56 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 29 and 31 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1298.56 Initial RMS Z values bonds: 1.50132 angles: 1.07504 torsions: N/A planes: 0.852012 non-bonded: 0 chiral vol: 0.433302 rama plot: -194.722 start_pos: N/A Minimum found (iteration number 345) at -1428.98 Final Estimated RMS Z Scores: bonds: 0.146761 angles: 0.255007 torsions: N/A planes: 0.625077 non-bonded: 0 chiral vol: 0.227586 rama plot: -201.684 start_pos: N/A SUCCESS TIME:: (dragged refinement): 119.57 Refinement elapsed time: 0.058 INFO:: replace_coords: 25 atoms updated. centering on B 31 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 30 and 32 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1376.27 Initial RMS Z values bonds: 0.627494 angles: 0.561674 torsions: N/A planes: 0.755656 non-bonded: 0 chiral vol: 0.159968 rama plot: -185.025 start_pos: N/A Minimum found (iteration number 67) at -1415.51 Final Estimated RMS Z Scores: bonds: 0.150483 angles: 0.458638 torsions: N/A planes: 0.598462 non-bonded: 0 chiral vol: 0.531256 rama plot: -196.486 start_pos: N/A SUCCESS TIME:: (dragged refinement): 120.245 Refinement elapsed time: 0.083 INFO:: replace_coords: 27 atoms updated. centering on B 32 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 3 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 31 and 33 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1345.85 Initial RMS Z values bonds: 0.589443 angles: 0.733868 torsions: N/A planes: 0.538707 non-bonded: 0.000195131 chiral vol: 0.515143 rama plot: -197.114 start_pos: N/A Minimum found (iteration number 324) at -1369.81 Final Estimated RMS Z Scores: bonds: 0.156125 angles: 0.448553 torsions: N/A planes: 0.436055 non-bonded: 0 chiral vol: 0.487178 rama plot: -197.266 start_pos: N/A SUCCESS TIME:: (dragged refinement): 120.908 Refinement elapsed time: 0.051 INFO:: replace_coords: 23 atoms updated. centering on B 33 CA created 18 bond restraints created 19 angle restraints created 2 plane restraints created 2 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 32 and 34 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1222.9 Initial RMS Z values bonds: 0.470762 angles: 0.475918 torsions: N/A planes: 0.585774 non-bonded: 0 chiral vol: 0.5905 rama plot: -174.947 start_pos: N/A Minimum found (iteration number 369) at -1238.52 Final Estimated RMS Z Scores: bonds: 0.124625 angles: 0.441726 torsions: N/A planes: 0.281995 non-bonded: 0 chiral vol: 0.543846 rama plot: -176.171 start_pos: N/A SUCCESS TIME:: (dragged refinement): 121.584 Refinement elapsed time: 0.055 INFO:: replace_coords: 21 atoms updated. centering on B 34 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 33 and 35 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1171.62 Initial RMS Z values bonds: 0.574192 angles: 0.66729 torsions: N/A planes: 0.534665 non-bonded: 0 chiral vol: 0.218959 rama plot: -172.77 start_pos: N/A Minimum found (iteration number 241) at -1187.54 Final Estimated RMS Z Scores: bonds: 0.145107 angles: 0.448821 torsions: N/A planes: 0.368546 non-bonded: 0 chiral vol: 0.123574 rama plot: -173.445 start_pos: N/A SUCCESS TIME:: (dragged refinement): 122.218 Refinement elapsed time: 0.032 INFO:: replace_coords: 19 atoms updated. centering on B 35 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 34 and 36 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1011.84 Initial RMS Z values bonds: 1.27568 angles: 0.669484 torsions: N/A planes: 0.57403 non-bonded: 0 chiral vol: 0.27379 rama plot: -173.647 start_pos: N/A Minimum found (iteration number 308) at -1053.18 Final Estimated RMS Z Scores: bonds: 0.10881 angles: 0.321458 torsions: N/A planes: 0.515969 non-bonded: 0 chiral vol: 0.117757 rama plot: -174.243 start_pos: N/A SUCCESS TIME:: (dragged refinement): 122.829 Refinement elapsed time: 0.039 INFO:: replace_coords: 18 atoms updated. centering on B 36 CA created 23 bond restraints created 27 angle restraints created 1 plane restraints created 3 chiral vol restraints created 54 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 35 and 37 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1198.49 Initial RMS Z values bonds: 0.678786 angles: 0.534416 torsions: N/A planes: 0.906019 non-bonded: 0 chiral vol: 0.665447 rama plot: -181.411 start_pos: N/A Minimum found (iteration number 327) at -1221.49 Final Estimated RMS Z Scores: bonds: 0.115361 angles: 0.328449 torsions: N/A planes: 0.944181 non-bonded: 0 chiral vol: 0.359453 rama plot: -181.8 start_pos: N/A SUCCESS TIME:: (dragged refinement): 123.394 Refinement elapsed time: 0.051 INFO:: replace_coords: 25 atoms updated. centering on B 37 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 36 and 38 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1164.89 Initial RMS Z values bonds: 0.615223 angles: 0.478145 torsions: N/A planes: 0.898677 non-bonded: 0 chiral vol: 0.471058 rama plot: -181.794 start_pos: N/A Minimum found (iteration number 251) at -1207.55 Final Estimated RMS Z Scores: bonds: 0.118092 angles: 0.357865 torsions: N/A planes: 0.591456 non-bonded: 0 chiral vol: 0.639462 rama plot: -193.741 start_pos: N/A SUCCESS TIME:: (dragged refinement): 124.065 Refinement elapsed time: 0.112 INFO:: replace_coords: 27 atoms updated. centering on B 38 CA created 26 bond restraints created 30 angle restraints created 3 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 37 and 39 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1179.68 Initial RMS Z values bonds: 0.411332 angles: 0.626582 torsions: N/A planes: 0.587626 non-bonded: 0 chiral vol: 0.69481 rama plot: -182.297 start_pos: N/A Minimum found (iteration number 105) at -1194.74 Final Estimated RMS Z Scores: bonds: 0.13024 angles: 0.508141 torsions: N/A planes: 0.682923 non-bonded: 0 chiral vol: 0.763295 rama plot: -184.328 start_pos: N/A SUCCESS TIME:: (dragged refinement): 124.673 Refinement elapsed time: 0.094 INFO:: replace_coords: 28 atoms updated. centering on B 39 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 38 and 40 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -940.669 Initial RMS Z values bonds: 0.5704 angles: 0.698526 torsions: N/A planes: 0.803041 non-bonded: 0.0817864 chiral vol: 0.734989 rama plot: -172.607 start_pos: N/A Minimum found (iteration number 63) at -1070.98 Final Estimated RMS Z Scores: bonds: 0.154808 angles: 0.504652 torsions: N/A planes: 0.838371 non-bonded: 2.44868e-07 chiral vol: 0.698101 rama plot: -197.19 start_pos: N/A SUCCESS TIME:: (dragged refinement): 125.501 Refinement elapsed time: 0.291 INFO:: replace_coords: 28 atoms updated. centering on B 40 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 39 and 41 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -973.047 Initial RMS Z values bonds: 0.439174 angles: 0.609159 torsions: N/A planes: 0.864908 non-bonded: 2.19415e-07 chiral vol: 0.706503 rama plot: -176.496 start_pos: N/A Minimum found (iteration number 368) at -1005.45 Final Estimated RMS Z Scores: bonds: 0.089675 angles: 0.354744 torsions: N/A planes: 0.845669 non-bonded: 1.18613e-07 chiral vol: 0.312866 rama plot: -183.483 start_pos: N/A SUCCESS TIME:: (dragged refinement): 126.177 Refinement elapsed time: 0.14 INFO:: replace_coords: 28 atoms updated. centering on B 41 CA created 23 bond restraints created 25 angle restraints created 2 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 40 and 42 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -905.988 Initial RMS Z values bonds: 0.266137 angles: 0.546943 torsions: N/A planes: 0.70117 non-bonded: 1.42642e-07 chiral vol: 0.389036 rama plot: -184.186 start_pos: N/A Minimum found (iteration number 2) at -920.503 Final Estimated RMS Z Scores: bonds: 0.0921967 angles: 0.325441 torsions: N/A planes: 0.666334 non-bonded: 3.64154e-08 chiral vol: 0.337368 rama plot: -185.238 start_pos: N/A SUCCESS TIME:: (dragged refinement): 126.793 Refinement elapsed time: 0.137 INFO:: replace_coords: 26 atoms updated. centering on B 42 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 41 and 43 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -938.038 Initial RMS Z values bonds: 0.44119 angles: 0.476133 torsions: N/A planes: 0.816055 non-bonded: 0 chiral vol: 0.436577 rama plot: -174.987 start_pos: N/A Minimum found (iteration number 1) at -976.929 Final Estimated RMS Z Scores: bonds: 0.0912577 angles: 0.323514 torsions: N/A planes: 0.819526 non-bonded: 0 chiral vol: 0.334173 rama plot: -185.517 start_pos: N/A SUCCESS TIME:: (dragged refinement): 127.365 Refinement elapsed time: 0.06 INFO:: replace_coords: 22 atoms updated. centering on B 43 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 42 and 44 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1036.96 Initial RMS Z values bonds: 0.903747 angles: 0.472143 torsions: N/A planes: 0.842045 non-bonded: 0 chiral vol: 0.246372 rama plot: -181.26 start_pos: N/A Minimum found (iteration number 297) at -1060.4 Final Estimated RMS Z Scores: bonds: 0.114983 angles: 0.332992 torsions: N/A planes: 0.902677 non-bonded: 0 chiral vol: 0.244404 rama plot: -182.443 start_pos: N/A SUCCESS TIME:: (dragged refinement): 127.936 Refinement elapsed time: 0.041 INFO:: replace_coords: 21 atoms updated. centering on B 44 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 3 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 43 and 45 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -640.833 Initial RMS Z values bonds: 0.776797 angles: 0.523924 torsions: N/A planes: 0.889732 non-bonded: 1.46843 chiral vol: 0.082762 rama plot: -186.351 start_pos: N/A Minimum found (iteration number 390) at -1020.11 Final Estimated RMS Z Scores: bonds: 1.58449 angles: 1.10735 torsions: N/A planes: 0.840784 non-bonded: 0.0984283 chiral vol: 0.15596 rama plot: -191.947 start_pos: N/A SUCCESS TIME:: (dragged refinement): 128.549 Refinement elapsed time: 0.058 INFO:: replace_coords: 22 atoms updated. centering on B 45 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 44 and 46 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1002.23 Initial RMS Z values bonds: 1.74031 angles: 1.39188 torsions: N/A planes: 0.630905 non-bonded: 0.103508 chiral vol: 0.522669 rama plot: -179.194 start_pos: N/A Minimum found (iteration number 303) at -1038.98 Final Estimated RMS Z Scores: bonds: 1.58195 angles: 1.10911 torsions: N/A planes: 0.668967 non-bonded: 0.103359 chiral vol: 0.183819 rama plot: -179.909 start_pos: N/A SUCCESS TIME:: (dragged refinement): 129.172 Refinement elapsed time: 0.045 INFO:: replace_coords: 22 atoms updated. centering on B 46 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 45 and 47 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1129.04 Initial RMS Z values bonds: 1.64581 angles: 1.26144 torsions: N/A planes: 0.737465 non-bonded: 0.000677687 chiral vol: 0.755374 rama plot: -177.411 start_pos: N/A Minimum found (iteration number 325) at -1254.26 Final Estimated RMS Z Scores: bonds: 0.150884 angles: 0.453565 torsions: N/A planes: 0.641824 non-bonded: 4.01275e-05 chiral vol: 0.244187 rama plot: -178.32 start_pos: N/A SUCCESS TIME:: (dragged refinement): 129.804 Refinement elapsed time: 0.05 INFO:: replace_coords: 23 atoms updated. centering on B 47 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 46 and 48 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1221.37 Initial RMS Z values bonds: 0.280007 angles: 0.580387 torsions: N/A planes: 1.02694 non-bonded: 0.000148143 chiral vol: 0.242965 rama plot: -169.194 start_pos: N/A Minimum found (iteration number 353) at -1256.4 Final Estimated RMS Z Scores: bonds: 0.172283 angles: 0.278896 torsions: N/A planes: 0.711051 non-bonded: 1.49131e-05 chiral vol: 0.181514 rama plot: -177.665 start_pos: N/A SUCCESS TIME:: (dragged refinement): 130.425 Refinement elapsed time: 0.05 INFO:: replace_coords: 22 atoms updated. centering on B 48 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 47 and 49 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1226.21 Initial RMS Z values bonds: 0.569435 angles: 0.563524 torsions: N/A planes: 0.76142 non-bonded: 1.09436e-05 chiral vol: 0.234397 rama plot: -164.129 start_pos: N/A unexpected error from gsl_multimin_fdfminimizer_iterate Error in gsl_multimin_fdfminimizer_iterate was GSL_ENOPROG Final Estimated RMS Z Scores bonds: 0.184646 angles: 0.378625 torsions: N/A planes: 0.281762 non-bonded: 1.92286e-05 chiral vol: 0.416592 rama plot: -175.712 start_pos: N/A NOPROGRESS TIME:: (dragged refinement): 131.025 Refinement elapsed time: 0.028 INFO:: replace_coords: 27 atoms updated. centering on B 49 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 2 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 48 and 50 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1068.38 Initial RMS Z values bonds: 0.519089 angles: 0.383743 torsions: N/A planes: 0.625616 non-bonded: 0 chiral vol: 0.494197 rama plot: -162.176 start_pos: N/A Minimum found (iteration number 56) at -1103.36 Final Estimated RMS Z Scores: bonds: 0.196501 angles: 0.430639 torsions: N/A planes: 0.525724 non-bonded: 0 chiral vol: 0.376234 rama plot: -172.221 start_pos: N/A SUCCESS TIME:: (dragged refinement): 131.578 Refinement elapsed time: 0.067 INFO:: replace_coords: 22 atoms updated. centering on B 50 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 49 and 51 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1273.53 Initial RMS Z values bonds: 0.783056 angles: 0.645251 torsions: N/A planes: 1.15532 non-bonded: 0 chiral vol: 1.10366 rama plot: -175.714 start_pos: N/A Minimum found (iteration number 390) at -1345.29 Final Estimated RMS Z Scores: bonds: 0.133916 angles: 0.280168 torsions: N/A planes: 0.750126 non-bonded: 0 chiral vol: 0.252172 rama plot: -185.805 start_pos: N/A SUCCESS TIME:: (dragged refinement): 132.123 Refinement elapsed time: 0.069 INFO:: replace_coords: 28 atoms updated. centering on B 51 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 50 and 52 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1399.2 Initial RMS Z values bonds: 1.12179 angles: 0.480681 torsions: N/A planes: 1.18521 non-bonded: 0 chiral vol: 1.02286 rama plot: -182.99 start_pos: N/A Minimum found (iteration number 254) at -1453.29 Final Estimated RMS Z Scores: bonds: 0.0970656 angles: 0.337595 torsions: N/A planes: 1.00023 non-bonded: 0 chiral vol: 0.292944 rama plot: -183.855 start_pos: N/A SUCCESS TIME:: (dragged refinement): 132.684 Refinement elapsed time: 0.051 INFO:: replace_coords: 28 atoms updated. centering on B 52 CA created 34 bond restraints created 42 angle restraints created 3 plane restraints created 3 chiral vol restraints created 82 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 51 and 53 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1627.26 Initial RMS Z values bonds: 0.297005 angles: 0.603312 torsions: N/A planes: 0.95227 non-bonded: 0 chiral vol: 0.316317 rama plot: -191.355 start_pos: N/A Minimum found (iteration number 162) at -1646.17 Final Estimated RMS Z Scores: bonds: 0.0999019 angles: 0.382064 torsions: N/A planes: 0.732594 non-bonded: 0 chiral vol: 0.245706 rama plot: -192.053 start_pos: N/A SUCCESS TIME:: (dragged refinement): 133.33 Refinement elapsed time: 0.121 INFO:: replace_coords: 34 atoms updated. centering on B 53 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 52 and 54 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1412.38 Initial RMS Z values bonds: 0.673337 angles: 0.695449 torsions: N/A planes: 0.803583 non-bonded: 0.0419934 chiral vol: 0.370562 rama plot: -176.076 start_pos: N/A Minimum found (iteration number 100) at -1464.75 Final Estimated RMS Z Scores: bonds: 0.127628 angles: 0.335061 torsions: N/A planes: 0.818438 non-bonded: 0 chiral vol: 0.327907 rama plot: -177.162 start_pos: N/A SUCCESS TIME:: (dragged refinement): 134.072 Refinement elapsed time: 0.164 INFO:: replace_coords: 31 atoms updated. centering on B 54 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 53 and 55 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1453.62 Initial RMS Z values bonds: 0.698367 angles: 0.689291 torsions: N/A planes: 0.848922 non-bonded: 0 chiral vol: 0.724372 rama plot: -175.2 start_pos: N/A Minimum found (iteration number 290) at -1498.47 Final Estimated RMS Z Scores: bonds: 0.149991 angles: 0.286322 torsions: N/A planes: 0.636723 non-bonded: 0 chiral vol: 0.286167 rama plot: -177.948 start_pos: N/A SUCCESS TIME:: (dragged refinement): 134.858 Refinement elapsed time: 0.138 INFO:: replace_coords: 31 atoms updated. centering on B 55 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 54 and 56 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1469.4 Initial RMS Z values bonds: 0.431844 angles: 0.66626 torsions: N/A planes: 1.16564 non-bonded: 0 chiral vol: 0.703294 rama plot: -177.579 start_pos: N/A Minimum found (iteration number 2) at -1501.36 Final Estimated RMS Z Scores: bonds: 0.173617 angles: 0.281271 torsions: N/A planes: 0.95738 non-bonded: 0 chiral vol: 0.244669 rama plot: -180.166 start_pos: N/A SUCCESS TIME:: (dragged refinement): 135.586 Refinement elapsed time: 0.074 INFO:: replace_coords: 28 atoms updated. centering on B 56 CA created 24 bond restraints created 29 angle restraints created 1 plane restraints created 4 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 55 and 57 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1417.42 Initial RMS Z values bonds: 0.962373 angles: 0.738213 torsions: N/A planes: 1.72167 non-bonded: 0 chiral vol: 0.697608 rama plot: -177.662 start_pos: N/A Minimum found (iteration number 242) at -1461.07 Final Estimated RMS Z Scores: bonds: 0.205677 angles: 0.615718 torsions: N/A planes: 1.51088 non-bonded: 0 chiral vol: 0.517462 rama plot: -179.374 start_pos: N/A SUCCESS TIME:: (dragged refinement): 136.304 Refinement elapsed time: 0.041 INFO:: replace_coords: 26 atoms updated. centering on B 57 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 56 and 58 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1278.42 Initial RMS Z values bonds: 0.691611 angles: 1.02853 torsions: N/A planes: 1.7384 non-bonded: 0 chiral vol: 0.885918 rama plot: -180.388 start_pos: N/A Minimum found (iteration number 351) at -1323.55 Final Estimated RMS Z Scores: bonds: 0.241248 angles: 0.54503 torsions: N/A planes: 1.44118 non-bonded: 3.63379e-05 chiral vol: 0.365275 rama plot: -180.338 start_pos: N/A SUCCESS TIME:: (dragged refinement): 137.05 Refinement elapsed time: 0.05 INFO:: replace_coords: 22 atoms updated. centering on B 58 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 57 and 59 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1249.96 Initial RMS Z values bonds: 0.329558 angles: 0.91879 torsions: N/A planes: 1.4867 non-bonded: 3.85809e-05 chiral vol: 0.804643 rama plot: -176.228 start_pos: N/A Minimum found (iteration number 311) at -1270.34 Final Estimated RMS Z Scores: bonds: 0.229244 angles: 0.599588 torsions: N/A planes: 1.47104 non-bonded: 5.79129e-05 chiral vol: 0.504522 rama plot: -176.919 start_pos: N/A SUCCESS TIME:: (dragged refinement): 137.79 Refinement elapsed time: 0.046 INFO:: replace_coords: 22 atoms updated. centering on B 59 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 5 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 58 and 60 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -689.259 Initial RMS Z values bonds: 0.700445 angles: 0.610354 torsions: N/A planes: 0.954897 non-bonded: 1.68294 chiral vol: 0.673925 rama plot: -180.149 start_pos: N/A Minimum found (iteration number 309) at -1144.52 Final Estimated RMS Z Scores: bonds: 1.5608 angles: 1.14355 torsions: N/A planes: 0.769146 non-bonded: 0.0952471 chiral vol: 0.257705 rama plot: -180.723 start_pos: N/A SUCCESS TIME:: (dragged refinement): 138.492 Refinement elapsed time: 0.046 INFO:: replace_coords: 22 atoms updated. centering on B 60 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 59 and 61 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -950.785 Initial RMS Z values bonds: 1.78362 angles: 1.28516 torsions: N/A planes: 0.700843 non-bonded: 0.145811 chiral vol: 0.331854 rama plot: -158.956 start_pos: N/A Minimum found (iteration number 325) at -984.176 Final Estimated RMS Z Scores: bonds: 1.70318 angles: 1.28038 torsions: N/A planes: 0.678939 non-bonded: 0.143807 chiral vol: 0.318004 rama plot: -169.318 start_pos: N/A SUCCESS TIME:: (dragged refinement): 139.201 Refinement elapsed time: 0.041 INFO:: replace_coords: 18 atoms updated. centering on B 61 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 60 and 62 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -879.728 Initial RMS Z values bonds: 1.95984 angles: 1.43412 torsions: N/A planes: 0.634991 non-bonded: 0 chiral vol: 0.0448733 rama plot: -170.53 start_pos: N/A Minimum found (iteration number 296) at -995.03 Final Estimated RMS Z Scores: bonds: 0.155508 angles: 0.643284 torsions: N/A planes: 0.50269 non-bonded: 0 chiral vol: 0.168626 rama plot: -170.276 start_pos: N/A SUCCESS TIME:: (dragged refinement): 139.886 Refinement elapsed time: 0.033 INFO:: replace_coords: 16 atoms updated. centering on B 62 CA created 17 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 61 and 63 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1074.56 Initial RMS Z values bonds: 0.866614 angles: 0.87001 torsions: N/A planes: 1.19282 non-bonded: 0.00277727 chiral vol: 0.427395 rama plot: -165.341 start_pos: N/A Minimum found (iteration number 366) at -1124.82 Final Estimated RMS Z Scores: bonds: 0.136182 angles: 0.405869 torsions: N/A planes: 0.768466 non-bonded: 0 chiral vol: 0.468121 rama plot: -169.069 start_pos: N/A SUCCESS TIME:: (dragged refinement): 140.568 Refinement elapsed time: 0.048 INFO:: replace_coords: 20 atoms updated. centering on B 63 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 62 and 64 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1208.48 Initial RMS Z values bonds: 0.198355 angles: 0.580702 torsions: N/A planes: 1.25819 non-bonded: 0 chiral vol: 0.448608 rama plot: -162.153 start_pos: N/A Minimum found (iteration number 377) at -1241.57 Final Estimated RMS Z Scores: bonds: 0.144311 angles: 0.406995 torsions: N/A planes: 0.910979 non-bonded: 4.89503e-05 chiral vol: 0.245447 rama plot: -172.783 start_pos: N/A SUCCESS TIME:: (dragged refinement): 141.331 Refinement elapsed time: 0.059 INFO:: replace_coords: 23 atoms updated. centering on B 64 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 63 and 65 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1338.71 Initial RMS Z values bonds: 1.00484 angles: 0.574049 torsions: N/A planes: 0.897916 non-bonded: 4.26918e-05 chiral vol: 0.274458 rama plot: -155.925 start_pos: N/A Minimum found (iteration number 357) at -1421.46 Final Estimated RMS Z Scores: bonds: 0.137207 angles: 0.324288 torsions: N/A planes: 0.555792 non-bonded: 0 chiral vol: 0.17926 rama plot: -167.989 start_pos: N/A SUCCESS TIME:: (dragged refinement): 142.141 Refinement elapsed time: 0.066 INFO:: replace_coords: 29 atoms updated. centering on B 65 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 64 and 66 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1137.34 Initial RMS Z values bonds: 0.772482 angles: 0.52161 torsions: N/A planes: 1.45802 non-bonded: 0 chiral vol: 0.149525 rama plot: -147.449 start_pos: N/A Minimum found (iteration number 319) at -1166.97 Final Estimated RMS Z Scores: bonds: 0.143691 angles: 0.433282 torsions: N/A planes: 1.08196 non-bonded: 0 chiral vol: 0.119188 rama plot: -150.087 start_pos: N/A SUCCESS TIME:: (dragged refinement): 142.903 Refinement elapsed time: 0.049 INFO:: replace_coords: 22 atoms updated. centering on B 66 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 65 and 67 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1150.54 Initial RMS Z values bonds: 0.731819 angles: 0.566548 torsions: N/A planes: 1.07443 non-bonded: 0 chiral vol: 0.638934 rama plot: -155.189 start_pos: N/A Minimum found (iteration number 294) at -1184.34 Final Estimated RMS Z Scores: bonds: 0.184569 angles: 0.629347 torsions: N/A planes: 0.820229 non-bonded: 0 chiral vol: 0.570906 rama plot: -163.902 start_pos: N/A SUCCESS TIME:: (dragged refinement): 143.603 Refinement elapsed time: 0.043 INFO:: replace_coords: 22 atoms updated. centering on B 67 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 66 and 68 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1188.85 Initial RMS Z values bonds: 0.875996 angles: 0.893306 torsions: N/A planes: 1.8133 non-bonded: 0.00464436 chiral vol: 0.581864 rama plot: -153.929 start_pos: N/A Minimum found (iteration number 1) at -1248.57 Final Estimated RMS Z Scores: bonds: 0.157656 angles: 0.536198 torsions: N/A planes: 0.98913 non-bonded: 0 chiral vol: 0.394167 rama plot: -155.146 start_pos: N/A SUCCESS TIME:: (dragged refinement): 144.306 Refinement elapsed time: 0.058 INFO:: replace_coords: 22 atoms updated. centering on B 68 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 67 and 69 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1478.12 Initial RMS Z values bonds: 1.17113 angles: 0.770903 torsions: N/A planes: 1.47238 non-bonded: 0 chiral vol: 0.483806 rama plot: -171.322 start_pos: N/A Minimum found (iteration number 286) at -1545.39 Final Estimated RMS Z Scores: bonds: 0.178002 angles: 0.364994 torsions: N/A planes: 1.37371 non-bonded: 0 chiral vol: 0.311817 rama plot: -173.565 start_pos: N/A SUCCESS TIME:: (dragged refinement): 145.052 Refinement elapsed time: 0.055 INFO:: replace_coords: 29 atoms updated. centering on B 69 CA created 27 bond restraints created 30 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 68 and 70 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1512.59 Initial RMS Z values bonds: 1.44818 angles: 0.663658 torsions: N/A planes: 1.38588 non-bonded: 0 chiral vol: 0.997495 rama plot: -178.676 start_pos: N/A Minimum found (iteration number 314) at -1596.44 Final Estimated RMS Z Scores: bonds: 0.184715 angles: 0.357383 torsions: N/A planes: 1.13233 non-bonded: 1.08241e-05 chiral vol: 0.184374 rama plot: -178.783 start_pos: N/A SUCCESS TIME:: (dragged refinement): 145.796 Refinement elapsed time: 0.057 INFO:: replace_coords: 30 atoms updated. centering on B 70 CA created 24 bond restraints created 27 angle restraints created 1 plane restraints created 5 chiral vol restraints created 57 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 69 and 71 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1397.25 Initial RMS Z values bonds: 0.842786 angles: 0.899052 torsions: N/A planes: 1.18415 non-bonded: 1.10759e-05 chiral vol: 0.365172 rama plot: -179.794 start_pos: N/A Minimum found (iteration number 247) at -1430.79 Final Estimated RMS Z Scores: bonds: 0.313086 angles: 0.588866 torsions: N/A planes: 1.17134 non-bonded: 5.17772e-05 chiral vol: 0.334438 rama plot: -179.918 start_pos: N/A SUCCESS TIME:: (dragged refinement): 146.595 Refinement elapsed time: 0.105 INFO:: replace_coords: 27 atoms updated. centering on B 71 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 5 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 70 and 72 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1175.92 Initial RMS Z values bonds: 0.625947 angles: 0.760265 torsions: N/A planes: 1.30468 non-bonded: 0.00237564 chiral vol: 0.734352 rama plot: -177.786 start_pos: N/A Minimum found (iteration number 366) at -1206.22 Final Estimated RMS Z Scores: bonds: 0.253315 angles: 0.457502 torsions: N/A planes: 1.26084 non-bonded: 5.90592e-05 chiral vol: 0.227677 rama plot: -180.993 start_pos: N/A SUCCESS TIME:: (dragged refinement): 147.29 Refinement elapsed time: 0.051 INFO:: replace_coords: 21 atoms updated. centering on B 72 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 71 and 73 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1045.68 Initial RMS Z values bonds: 0.383912 angles: 0.808079 torsions: N/A planes: 0.815282 non-bonded: 2.77586e-05 chiral vol: 0.277698 rama plot: -168.816 start_pos: N/A Minimum found (iteration number 384) at -1061.59 Final Estimated RMS Z Scores: bonds: 0.197903 angles: 0.718115 torsions: N/A planes: 0.847266 non-bonded: 3.29614e-05 chiral vol: 0.191073 rama plot: -173.62 start_pos: N/A SUCCESS TIME:: (dragged refinement): 147.908 Refinement elapsed time: 0.041 INFO:: replace_coords: 17 atoms updated. centering on B 73 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 72 and 74 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1014.68 Initial RMS Z values bonds: 0.530372 angles: 0.779185 torsions: N/A planes: 0.886428 non-bonded: 0.00528496 chiral vol: 0.175706 rama plot: -177.219 start_pos: N/A Minimum found (iteration number 105) at -1049.84 Final Estimated RMS Z Scores: bonds: 0.250679 angles: 0.449538 torsions: N/A planes: 1.03683 non-bonded: 0 chiral vol: 0.366945 rama plot: -185.788 start_pos: N/A SUCCESS TIME:: (dragged refinement): 148.472 Refinement elapsed time: 0.061 INFO:: replace_coords: 18 atoms updated. centering on B 74 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 73 and 75 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -989.149 Initial RMS Z values bonds: 0.387406 angles: 0.519602 torsions: N/A planes: 1.11266 non-bonded: 0 chiral vol: 0.46569 rama plot: -184.144 start_pos: N/A Minimum found (iteration number 380) at -1004.37 Final Estimated RMS Z Scores: bonds: 0.175548 angles: 0.410358 torsions: N/A planes: 0.870655 non-bonded: 0 chiral vol: 0.430752 rama plot: -187.075 start_pos: N/A SUCCESS TIME:: (dragged refinement): 149 Refinement elapsed time: 0.046 INFO:: replace_coords: 18 atoms updated. centering on B 75 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 74 and 76 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1011.73 Initial RMS Z values bonds: 0.45653 angles: 0.585265 torsions: N/A planes: 0.699455 non-bonded: 0 chiral vol: 0.619328 rama plot: -193.711 start_pos: N/A Minimum found (iteration number 362) at -1032.65 Final Estimated RMS Z Scores: bonds: 0.119983 angles: 0.212158 torsions: N/A planes: 0.356505 non-bonded: 0 chiral vol: 0.279205 rama plot: -195.087 start_pos: N/A SUCCESS TIME:: (dragged refinement): 149.479 Refinement elapsed time: 0.048 INFO:: replace_coords: 21 atoms updated. centering on B 76 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 75 and 77 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -884.898 Initial RMS Z values bonds: 0.63257 angles: 0.757106 torsions: N/A planes: 0.531848 non-bonded: 0 chiral vol: 0.396285 rama plot: -169.259 start_pos: N/A Minimum found (iteration number 223) at -917.94 Final Estimated RMS Z Scores: bonds: 0.162582 angles: 0.287894 torsions: N/A planes: 0.451849 non-bonded: 4.01081e-06 chiral vol: 0.14118 rama plot: -173.019 start_pos: N/A SUCCESS TIME:: (dragged refinement): 149.979 Refinement elapsed time: 0.086 INFO:: replace_coords: 21 atoms updated. centering on B 77 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 76 and 78 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1065.86 Initial RMS Z values bonds: 0.471253 angles: 0.578605 torsions: N/A planes: 0.57054 non-bonded: 3.05392e-06 chiral vol: 0.168461 rama plot: -159.591 start_pos: N/A Minimum found (iteration number 172) at -1077.98 Final Estimated RMS Z Scores: bonds: 0.22565 angles: 0.40994 torsions: N/A planes: 0.389441 non-bonded: 4.41533e-06 chiral vol: 0.128386 rama plot: -160.08 start_pos: N/A SUCCESS TIME:: (dragged refinement): 150.54 Refinement elapsed time: 0.092 INFO:: replace_coords: 25 atoms updated. centering on B 78 CA created 23 bond restraints created 26 angle restraints created 3 plane restraints created 3 chiral vol restraints created 55 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 77 and 79 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1205.52 Initial RMS Z values bonds: 0.34636 angles: 0.738674 torsions: N/A planes: 0.507606 non-bonded: 0 chiral vol: 0.831849 rama plot: -156.06 start_pos: N/A Minimum found (iteration number 324) at -1234.75 Final Estimated RMS Z Scores: bonds: 0.215399 angles: 0.360776 torsions: N/A planes: 0.439812 non-bonded: 0 chiral vol: 0.208237 rama plot: -159.414 start_pos: N/A SUCCESS TIME:: (dragged refinement): 151.1 Refinement elapsed time: 0.056 INFO:: replace_coords: 26 atoms updated. centering on B 79 CA created 27 bond restraints created 32 angle restraints created 3 plane restraints created 3 chiral vol restraints created 65 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 78 and 80 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1442.74 Initial RMS Z values bonds: 0.774886 angles: 0.733629 torsions: N/A planes: 1.07548 non-bonded: 0 chiral vol: 0.600636 rama plot: -164.553 start_pos: N/A Minimum found (iteration number 264) at -1491.7 Final Estimated RMS Z Scores: bonds: 0.208877 angles: 0.460938 torsions: N/A planes: 0.34158 non-bonded: 0 chiral vol: 0.265204 rama plot: -166.949 start_pos: N/A SUCCESS TIME:: (dragged refinement): 151.749 Refinement elapsed time: 0.055 INFO:: replace_coords: 29 atoms updated. centering on B 80 CA created 31 bond restraints created 38 angle restraints created 3 plane restraints created 3 chiral vol restraints created 75 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 79 and 81 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1569.82 Initial RMS Z values bonds: 0.775342 angles: 0.573443 torsions: N/A planes: 1.23007 non-bonded: 0.00163042 chiral vol: 0.606463 rama plot: -178.736 start_pos: N/A Minimum found (iteration number 281) at -1616.19 Final Estimated RMS Z Scores: bonds: 0.253837 angles: 0.302101 torsions: N/A planes: 0.723599 non-bonded: 0 chiral vol: 0.137888 rama plot: -180.897 start_pos: N/A SUCCESS TIME:: (dragged refinement): 152.456 Refinement elapsed time: 0.058 INFO:: replace_coords: 32 atoms updated. centering on B 81 CA created 30 bond restraints created 37 angle restraints created 2 plane restraints created 4 chiral vol restraints created 73 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 80 and 82 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1577.85 Initial RMS Z values bonds: 0.683887 angles: 0.573686 torsions: N/A planes: 1.09592 non-bonded: 0 chiral vol: 0.478809 rama plot: -180.091 start_pos: N/A Minimum found (iteration number 203) at -1613.86 Final Estimated RMS Z Scores: bonds: 0.17027 angles: 0.269512 torsions: N/A planes: 0.734667 non-bonded: 0 chiral vol: 0.159243 rama plot: -180.774 start_pos: N/A SUCCESS TIME:: (dragged refinement): 153.215 Refinement elapsed time: 0.042 INFO:: replace_coords: 31 atoms updated. centering on B 82 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 81 and 83 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1347.9 Initial RMS Z values bonds: 0.428097 angles: 0.347348 torsions: N/A planes: 0.869674 non-bonded: 0 chiral vol: 0.148871 rama plot: -176.294 start_pos: N/A Minimum found (iteration number 249) at -1359.1 Final Estimated RMS Z Scores: bonds: 0.186445 angles: 0.225666 torsions: N/A planes: 0.899491 non-bonded: 0 chiral vol: 0.0910612 rama plot: -178.325 start_pos: N/A SUCCESS TIME:: (dragged refinement): 153.955 Refinement elapsed time: 0.039 INFO:: replace_coords: 23 atoms updated. centering on B 83 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 82 and 84 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1146.16 Initial RMS Z values bonds: 0.518237 angles: 0.781302 torsions: N/A planes: 1.16029 non-bonded: 0 chiral vol: 0.148783 rama plot: -159.32 start_pos: N/A Minimum found (iteration number 240) at -1182.85 Final Estimated RMS Z Scores: bonds: 0.153204 angles: 0.428361 torsions: N/A planes: 0.901277 non-bonded: 0 chiral vol: 0.691939 rama plot: -166.435 start_pos: N/A SUCCESS TIME:: (dragged refinement): 154.653 Refinement elapsed time: 0.034 INFO:: replace_coords: 19 atoms updated. centering on B 84 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 2 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 83 and 85 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1049.37 Initial RMS Z values bonds: 0.514511 angles: 0.570883 torsions: N/A planes: 0.953476 non-bonded: 0 chiral vol: 0.843855 rama plot: -148.692 start_pos: N/A Minimum found (iteration number 232) at -1084.46 Final Estimated RMS Z Scores: bonds: 0.140708 angles: 0.388255 torsions: N/A planes: 0.776455 non-bonded: 0 chiral vol: 0.862216 rama plot: -154.441 start_pos: N/A SUCCESS TIME:: (dragged refinement): 155.331 Refinement elapsed time: 0.091 INFO:: replace_coords: 22 atoms updated. centering on B 85 CA created 29 bond restraints created 35 angle restraints created 3 plane restraints created 3 chiral vol restraints created 70 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 84 and 86 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1139.86 Initial RMS Z values bonds: 0.544089 angles: 0.539642 torsions: N/A planes: 0.845011 non-bonded: 0 chiral vol: 0.847888 rama plot: -148.159 start_pos: N/A Minimum found (iteration number 243) at -1157.62 Final Estimated RMS Z Scores: bonds: 0.127909 angles: 0.426201 torsions: N/A planes: 0.765884 non-bonded: 9.74949e-07 chiral vol: 0.787085 rama plot: -148.598 start_pos: N/A SUCCESS TIME:: (dragged refinement): 156.07 Refinement elapsed time: 0.132 INFO:: replace_coords: 30 atoms updated. centering on B 86 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 85 and 87 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1081.01 Initial RMS Z values bonds: 0.83696 angles: 0.463154 torsions: N/A planes: 0.710444 non-bonded: 1.23067e-06 chiral vol: 0.542091 rama plot: -171.796 start_pos: N/A Minimum found (iteration number 179) at -1115.78 Final Estimated RMS Z Scores: bonds: 0.156075 angles: 0.426078 torsions: N/A planes: 0.680382 non-bonded: 6.99731e-07 chiral vol: 0.534858 rama plot: -177.466 start_pos: N/A SUCCESS TIME:: (dragged refinement): 156.773 Refinement elapsed time: 0.105 INFO:: replace_coords: 27 atoms updated. centering on B 87 CA created 22 bond restraints created 26 angle restraints created 1 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 86 and 88 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1129.48 Initial RMS Z values bonds: 0.518976 angles: 0.812992 torsions: N/A planes: 0.720396 non-bonded: 0 chiral vol: 0.768959 rama plot: -183.735 start_pos: N/A Minimum found (iteration number 321) at -1160.54 Final Estimated RMS Z Scores: bonds: 0.12681 angles: 0.387178 torsions: N/A planes: 0.702985 non-bonded: 0 chiral vol: 0.331105 rama plot: -184.527 start_pos: N/A SUCCESS TIME:: (dragged refinement): 157.326 Refinement elapsed time: 0.049 INFO:: replace_coords: 24 atoms updated. centering on B 88 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 87 and 89 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1253.8 Initial RMS Z values bonds: 0.855721 angles: 0.568174 torsions: N/A planes: 1.17673 non-bonded: 0 chiral vol: 0.379764 rama plot: -191.038 start_pos: N/A Minimum found (iteration number 324) at -1284.49 Final Estimated RMS Z Scores: bonds: 0.0978125 angles: 0.299815 torsions: N/A planes: 1.07606 non-bonded: 0 chiral vol: 0.129249 rama plot: -191.635 start_pos: N/A SUCCESS TIME:: (dragged refinement): 157.971 Refinement elapsed time: 0.05 INFO:: replace_coords: 23 atoms updated. centering on B 89 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 4 chiral vol restraints created 52 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 88 and 90 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1312.85 Initial RMS Z values bonds: 0.440041 angles: 0.485584 torsions: N/A planes: 1.02347 non-bonded: 0 chiral vol: 0.343845 rama plot: -177.045 start_pos: N/A Minimum found (iteration number 349) at -1331.6 Final Estimated RMS Z Scores: bonds: 0.118286 angles: 0.278619 torsions: N/A planes: 0.56389 non-bonded: 0 chiral vol: 0.196951 rama plot: -178.547 start_pos: N/A SUCCESS TIME:: (dragged refinement): 158.685 Refinement elapsed time: 0.055 INFO:: replace_coords: 24 atoms updated. centering on B 90 CA created 23 bond restraints created 26 angle restraints created 1 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 89 and 91 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1302.14 Initial RMS Z values bonds: 0.607979 angles: 0.708306 torsions: N/A planes: 0.621174 non-bonded: 0 chiral vol: 1.02352 rama plot: -177.92 start_pos: N/A Minimum found (iteration number 279) at -1325.41 Final Estimated RMS Z Scores: bonds: 0.125141 angles: 0.454613 torsions: N/A planes: 0.778776 non-bonded: 0 chiral vol: 0.349364 rama plot: -179.404 start_pos: N/A SUCCESS TIME:: (dragged refinement): 159.402 Refinement elapsed time: 0.045 INFO:: replace_coords: 25 atoms updated. centering on B 91 CA created 19 bond restraints created 21 angle restraints created 0 plane restraints created 4 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 90 and 92 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1179.68 Initial RMS Z values bonds: 1.08776 angles: 0.739074 torsions: N/A planes: 1.03766 non-bonded: 0.0179055 chiral vol: 0.40555 rama plot: -177.953 start_pos: N/A Minimum found (iteration number 373) at -1225.27 Final Estimated RMS Z Scores: bonds: 0.169991 angles: 0.39144 torsions: N/A planes: 1.01929 non-bonded: 0 chiral vol: 0.242762 rama plot: -178.106 start_pos: N/A SUCCESS TIME:: (dragged refinement): 160.088 Refinement elapsed time: 0.054 INFO:: replace_coords: 22 atoms updated. centering on B 92 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 91 and 93 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1277.84 Initial RMS Z values bonds: 0.501512 angles: 0.672811 torsions: N/A planes: 1.00893 non-bonded: 0 chiral vol: 0.648674 rama plot: -172.587 start_pos: N/A Minimum found (iteration number 265) at -1300.2 Final Estimated RMS Z Scores: bonds: 0.194911 angles: 0.474379 torsions: N/A planes: 0.83263 non-bonded: 0 chiral vol: 0.375586 rama plot: -174.189 start_pos: N/A SUCCESS TIME:: (dragged refinement): 160.751 Refinement elapsed time: 0.046 INFO:: replace_coords: 24 atoms updated. centering on B 93 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 92 and 94 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1297.41 Initial RMS Z values bonds: 0.508623 angles: 0.56974 torsions: N/A planes: 0.850602 non-bonded: 0 chiral vol: 0.4634 rama plot: -172.48 start_pos: N/A Minimum found (iteration number 327) at -1317.91 Final Estimated RMS Z Scores: bonds: 0.159653 angles: 0.354568 torsions: N/A planes: 0.883023 non-bonded: 0 chiral vol: 0.349036 rama plot: -175.196 start_pos: N/A SUCCESS TIME:: (dragged refinement): 161.352 Refinement elapsed time: 0.056 INFO:: replace_coords: 25 atoms updated. centering on B 94 CA created 21 bond restraints created 24 angle restraints created 2 plane restraints created 4 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 93 and 95 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1272.67 Initial RMS Z values bonds: 0.477112 angles: 0.585475 torsions: N/A planes: 0.999728 non-bonded: 0 chiral vol: 0.469944 rama plot: -173.661 start_pos: N/A Minimum found (iteration number 334) at -1294.06 Final Estimated RMS Z Scores: bonds: 0.151571 angles: 0.415576 torsions: N/A planes: 0.766803 non-bonded: 0 chiral vol: 0.468504 rama plot: -176.119 start_pos: N/A SUCCESS TIME:: (dragged refinement): 161.931 Refinement elapsed time: 0.055 INFO:: replace_coords: 24 atoms updated. centering on B 95 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 94 and 96 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -964.835 Initial RMS Z values bonds: 0.721642 angles: 0.511847 torsions: N/A planes: 0.681111 non-bonded: 0 chiral vol: 0.418475 rama plot: -177.211 start_pos: N/A Minimum found (iteration number 316) at -982.745 Final Estimated RMS Z Scores: bonds: 0.135782 angles: 0.327336 torsions: N/A planes: 0.568631 non-bonded: 0 chiral vol: 0.413067 rama plot: -176.572 start_pos: N/A SUCCESS TIME:: (dragged refinement): 162.483 Refinement elapsed time: 0.041 INFO:: replace_coords: 22 atoms updated. centering on B 96 CA created 11 bond restraints created 12 angle restraints created 0 plane restraints created 3 chiral vol restraints created 26 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 95 and 96 of chain B Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -556.562 Initial RMS Z values bonds: 0.136893 angles: 0.353351 torsions: N/A planes: 0.116429 non-bonded: 0 chiral vol: 0.419269 rama plot: N/A start_pos: N/A Minimum found (iteration number 227) at -557.55 Final Estimated RMS Z Scores: bonds: 0.119397 angles: 0.324362 torsions: N/A planes: 0.353587 non-bonded: 0 chiral vol: 0.347418 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 163.052 Refinement elapsed time: 0.017 INFO:: replace_coords: 13 atoms updated. There are 93 residues in chain A centering on A 1 CA created 13 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -189.834 Initial RMS Z values bonds: 0.0988585 angles: 0.720922 torsions: N/A planes: 0.99678 non-bonded: 0.0550638 chiral vol: 0.375438 rama plot: N/A start_pos: N/A Minimum found (iteration number 2) at -201.491 Final Estimated RMS Z Scores: bonds: 0.10772 angles: 0.519607 torsions: N/A planes: 1.06035 non-bonded: 0.00011427 chiral vol: 0.28514 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 163.708 Refinement elapsed time: 0.062 INFO:: replace_coords: 15 atoms updated. centering on A 2 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 1 and 3 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -331.065 Initial RMS Z values bonds: 0.143196 angles: 0.541799 torsions: N/A planes: 0.918831 non-bonded: 5.71348e-05 chiral vol: 0.514332 rama plot: -27.3742 start_pos: N/A Minimum found (iteration number 143) at -358.936 Final Estimated RMS Z Scores: bonds: 0.130755 angles: 0.634285 torsions: N/A planes: 1.20626 non-bonded: 0.000395237 chiral vol: 0.520991 rama plot: -52.3123 start_pos: N/A SUCCESS TIME:: (dragged refinement): 164.396 Refinement elapsed time: 0.112 INFO:: replace_coords: 21 atoms updated. centering on A 3 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 2 and 4 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -696.475 Initial RMS Z values bonds: 0.20275 angles: 0.686337 torsions: N/A planes: 1.15851 non-bonded: 0 chiral vol: 0.637825 rama plot: -114.448 start_pos: N/A Minimum found (iteration number 128) at -734.87 Final Estimated RMS Z Scores: bonds: 0.224319 angles: 0.677139 torsions: N/A planes: 0.914035 non-bonded: 0 chiral vol: 0.678647 rama plot: -129.344 start_pos: N/A SUCCESS TIME:: (dragged refinement): 164.95 Refinement elapsed time: 0.061 INFO:: replace_coords: 17 atoms updated. centering on A 4 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 3 and 5 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -940.061 Initial RMS Z values bonds: 0.245564 angles: 0.415407 torsions: N/A planes: 0.925359 non-bonded: 0 chiral vol: 0.484378 rama plot: -172.819 start_pos: N/A Minimum found (iteration number 216) at -941.368 Final Estimated RMS Z Scores: bonds: 0.203915 angles: 0.387466 torsions: N/A planes: 0.936263 non-bonded: 0 chiral vol: 0.456757 rama plot: -172.764 start_pos: N/A SUCCESS TIME:: (dragged refinement): 165.49 Refinement elapsed time: 0.027 INFO:: replace_coords: 17 atoms updated. centering on A 5 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 4 and 6 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1041.85 Initial RMS Z values bonds: 0.22296 angles: 0.334086 torsions: N/A planes: 0.517801 non-bonded: 0 chiral vol: 0.159054 rama plot: -159.04 start_pos: N/A Minimum found (iteration number 214) at -1042.47 Final Estimated RMS Z Scores: bonds: 0.196956 angles: 0.314214 torsions: N/A planes: 0.489524 non-bonded: 0 chiral vol: 0.155301 rama plot: -159.13 start_pos: N/A SUCCESS TIME:: (dragged refinement): 166.119 Refinement elapsed time: 0.029 INFO:: replace_coords: 18 atoms updated. centering on A 6 CA created 17 bond restraints created 19 angle restraints created 0 plane restraints created 4 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 5 and 7 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1402.91 Initial RMS Z values bonds: 0.168083 angles: 0.281525 torsions: N/A planes: 0.517351 non-bonded: 0 chiral vol: 0.138934 rama plot: -181.966 start_pos: N/A Minimum found (iteration number 275) at -1405.23 Final Estimated RMS Z Scores: bonds: 0.184192 angles: 0.27067 torsions: N/A planes: 0.424439 non-bonded: 0 chiral vol: 0.144499 rama plot: -182.397 start_pos: N/A SUCCESS TIME:: (dragged refinement): 166.768 Refinement elapsed time: 0.036 INFO:: replace_coords: 20 atoms updated. centering on A 7 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 6 and 8 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1520.67 Initial RMS Z values bonds: 0.168488 angles: 0.201222 torsions: N/A planes: 0.44808 non-bonded: 0 chiral vol: 0.189929 rama plot: -192.938 start_pos: N/A Minimum found (iteration number 262) at -1525.9 Final Estimated RMS Z Scores: bonds: 0.226713 angles: 0.247912 torsions: N/A planes: 0.33808 non-bonded: 0 chiral vol: 0.229975 rama plot: -194.761 start_pos: N/A SUCCESS TIME:: (dragged refinement): 167.415 Refinement elapsed time: 0.037 INFO:: replace_coords: 21 atoms updated. centering on A 8 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 3 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 7 and 9 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1522.34 Initial RMS Z values bonds: 0.222677 angles: 0.352746 torsions: N/A planes: 0.291915 non-bonded: 0 chiral vol: 0.269421 rama plot: -205.098 start_pos: N/A Minimum found (iteration number 242) at -1526.2 Final Estimated RMS Z Scores: bonds: 0.181634 angles: 0.287011 torsions: N/A planes: 0.362192 non-bonded: 0 chiral vol: 0.190897 rama plot: -206.223 start_pos: N/A SUCCESS TIME:: (dragged refinement): 168.09 Refinement elapsed time: 0.035 INFO:: replace_coords: 20 atoms updated. centering on A 9 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 8 and 10 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1289.32 Initial RMS Z values bonds: 0.183331 angles: 0.368608 torsions: N/A planes: 0.532783 non-bonded: 0 chiral vol: 0.348426 rama plot: -216.723 start_pos: N/A Minimum found (iteration number 226) at -1292.66 Final Estimated RMS Z Scores: bonds: 0.212905 angles: 0.368335 torsions: N/A planes: 0.609942 non-bonded: 0 chiral vol: 0.349621 rama plot: -217.938 start_pos: N/A SUCCESS TIME:: (dragged refinement): 168.648 Refinement elapsed time: 0.034 INFO:: replace_coords: 19 atoms updated. centering on A 10 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 9 and 11 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1196 Initial RMS Z values bonds: 0.212918 angles: 0.428738 torsions: N/A planes: 0.726081 non-bonded: 0 chiral vol: 0.384181 rama plot: -200.188 start_pos: N/A Minimum found (iteration number 284) at -1206.09 Final Estimated RMS Z Scores: bonds: 0.243615 angles: 0.416068 torsions: N/A planes: 0.551605 non-bonded: 0 chiral vol: 0.367169 rama plot: -203.862 start_pos: N/A SUCCESS TIME:: (dragged refinement): 169.196 Refinement elapsed time: 0.038 INFO:: replace_coords: 19 atoms updated. centering on A 11 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 10 and 12 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -541.22 Initial RMS Z values bonds: 0.223323 angles: 0.42267 torsions: N/A planes: 0.740805 non-bonded: 2.20651 chiral vol: 0.364886 rama plot: -185.843 start_pos: N/A Minimum found (iteration number 378) at -1027.92 Final Estimated RMS Z Scores: bonds: 1.65848 angles: 1.1834 torsions: N/A planes: 0.83378 non-bonded: 0.117778 chiral vol: 0.381384 rama plot: -189.837 start_pos: N/A SUCCESS TIME:: (dragged refinement): 169.796 Refinement elapsed time: 0.053 INFO:: replace_coords: 20 atoms updated. centering on A 12 CA created 21 bond restraints created 24 angle restraints created 0 plane restraints created 3 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 11 and 13 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -398.396 Initial RMS Z values bonds: 1.55772 angles: 1.12714 torsions: N/A planes: 0.909651 non-bonded: 2.26569 chiral vol: 0.264508 rama plot: -181.569 start_pos: N/A Minimum found (iteration number 39) at -939.067 Final Estimated RMS Z Scores: bonds: 2.15985 angles: 1.54341 torsions: N/A planes: 0.720734 non-bonded: 0.211376 chiral vol: 0.26287 rama plot: -183.755 start_pos: N/A SUCCESS TIME:: (dragged refinement): 170.384 Refinement elapsed time: 0.064 INFO:: replace_coords: 22 atoms updated. centering on A 13 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 3 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 12 and 14 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1065.02 Initial RMS Z values bonds: 2.11768 angles: 1.51412 torsions: N/A planes: 0.571373 non-bonded: 0.0827243 chiral vol: 0.212222 rama plot: -189.001 start_pos: N/A Minimum found (iteration number 1) at -1183.74 Final Estimated RMS Z Scores: bonds: 1.50837 angles: 1.08777 torsions: N/A planes: 0.686253 non-bonded: 0.0824155 chiral vol: 0.14584 rama plot: -195.902 start_pos: N/A SUCCESS TIME:: (dragged refinement): 170.99 Refinement elapsed time: 0.062 INFO:: replace_coords: 23 atoms updated. centering on A 14 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 13 and 15 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1246.89 Initial RMS Z values bonds: 1.60286 angles: 1.12787 torsions: N/A planes: 0.602454 non-bonded: 0 chiral vol: 0.150231 rama plot: -208.067 start_pos: N/A Minimum found (iteration number 357) at -1357.7 Final Estimated RMS Z Scores: bonds: 0.178591 angles: 0.335586 torsions: N/A planes: 0.635837 non-bonded: 0 chiral vol: 0.103153 rama plot: -212.459 start_pos: N/A SUCCESS TIME:: (dragged refinement): 171.649 Refinement elapsed time: 0.052 INFO:: replace_coords: 21 atoms updated. centering on A 15 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 14 and 16 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1435.75 Initial RMS Z values bonds: 0.156609 angles: 0.235219 torsions: N/A planes: 0.417465 non-bonded: 0 chiral vol: 0.0925818 rama plot: -216.571 start_pos: N/A Minimum found (iteration number 262) at -1439.58 Final Estimated RMS Z Scores: bonds: 0.1138 angles: 0.245985 torsions: N/A planes: 0.463957 non-bonded: 0 chiral vol: 0.168303 rama plot: -218.362 start_pos: N/A SUCCESS TIME:: (dragged refinement): 172.368 Refinement elapsed time: 0.038 INFO:: replace_coords: 21 atoms updated. centering on A 16 CA created 17 bond restraints created 19 angle restraints created 1 plane restraints created 4 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 15 and 17 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1465.51 Initial RMS Z values bonds: 0.111254 angles: 0.240082 torsions: N/A planes: 0.321895 non-bonded: 0 chiral vol: 0.204754 rama plot: -219.663 start_pos: N/A Minimum found (iteration number 231) at -1468.92 Final Estimated RMS Z Scores: bonds: 0.114017 angles: 0.23424 torsions: N/A planes: 0.340036 non-bonded: 0 chiral vol: 0.186036 rama plot: -220.791 start_pos: N/A SUCCESS TIME:: (dragged refinement): 173.089 Refinement elapsed time: 0.033 INFO:: replace_coords: 20 atoms updated. centering on A 17 CA created 19 bond restraints created 22 angle restraints created 1 plane restraints created 5 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 16 and 18 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1562.91 Initial RMS Z values bonds: 0.124991 angles: 0.253347 torsions: N/A planes: 0.313839 non-bonded: 0 chiral vol: 0.17029 rama plot: -220.301 start_pos: N/A Minimum found (iteration number 187) at -1564.04 Final Estimated RMS Z Scores: bonds: 0.130941 angles: 0.256414 torsions: N/A planes: 0.270784 non-bonded: 0 chiral vol: 0.199322 rama plot: -220.447 start_pos: N/A SUCCESS TIME:: (dragged refinement): 173.804 Refinement elapsed time: 0.03 INFO:: replace_coords: 22 atoms updated. centering on A 18 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 17 and 19 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1568.92 Initial RMS Z values bonds: 0.117994 angles: 0.26637 torsions: N/A planes: 0.188761 non-bonded: 0 chiral vol: 0.227361 rama plot: -220.416 start_pos: N/A Minimum found (iteration number 184) at -1569.31 Final Estimated RMS Z Scores: bonds: 0.124536 angles: 0.27878 torsions: N/A planes: 0.172652 non-bonded: 0 chiral vol: 0.228854 rama plot: -220.493 start_pos: N/A SUCCESS TIME:: (dragged refinement): 174.521 Refinement elapsed time: 0.032 INFO:: replace_coords: 23 atoms updated. centering on A 19 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 18 and 20 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1498.45 Initial RMS Z values bonds: 0.133572 angles: 0.24533 torsions: N/A planes: 0.23579 non-bonded: 0 chiral vol: 0.145239 rama plot: -221.03 start_pos: N/A Minimum found (iteration number 216) at -1499.69 Final Estimated RMS Z Scores: bonds: 0.125859 angles: 0.222567 torsions: N/A planes: 0.266894 non-bonded: 0 chiral vol: 0.111466 rama plot: -221.402 start_pos: N/A SUCCESS TIME:: (dragged refinement): 175.318 Refinement elapsed time: 0.036 INFO:: replace_coords: 23 atoms updated. centering on A 20 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 19 and 21 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1484.58 Initial RMS Z values bonds: 0.13494 angles: 0.229748 torsions: N/A planes: 0.263788 non-bonded: 0 chiral vol: 0.14712 rama plot: -221.263 start_pos: N/A Minimum found (iteration number 231) at -1484.95 Final Estimated RMS Z Scores: bonds: 0.133766 angles: 0.236008 torsions: N/A planes: 0.256979 non-bonded: 0 chiral vol: 0.143351 rama plot: -221.383 start_pos: N/A SUCCESS TIME:: (dragged refinement): 176.049 Refinement elapsed time: 0.04 INFO:: replace_coords: 24 atoms updated. centering on A 21 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 20 and 22 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1461.32 Initial RMS Z values bonds: 0.134247 angles: 0.233415 torsions: N/A planes: 0.257171 non-bonded: 5.51644e-06 chiral vol: 0.139062 rama plot: -221.423 start_pos: N/A Minimum found (iteration number 200) at -1461.64 Final Estimated RMS Z Scores: bonds: 0.136106 angles: 0.217758 torsions: N/A planes: 0.263847 non-bonded: 6.33531e-06 chiral vol: 0.128981 rama plot: -221.406 start_pos: N/A SUCCESS TIME:: (dragged refinement): 176.703 Refinement elapsed time: 0.035 INFO:: replace_coords: 24 atoms updated. centering on A 22 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 4 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 21 and 23 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1357.78 Initial RMS Z values bonds: 0.135832 angles: 0.229722 torsions: N/A planes: 0.366544 non-bonded: 8.37476e-06 chiral vol: 0.127562 rama plot: -220.876 start_pos: N/A Minimum found (iteration number 220) at -1358.68 Final Estimated RMS Z Scores: bonds: 0.130212 angles: 0.219577 torsions: N/A planes: 0.413742 non-bonded: 1.94925e-05 chiral vol: 0.123551 rama plot: -221.249 start_pos: N/A SUCCESS TIME:: (dragged refinement): 177.379 Refinement elapsed time: 0.032 INFO:: replace_coords: 21 atoms updated. centering on A 23 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 4 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 22 and 24 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1212.54 Initial RMS Z values bonds: 0.121674 angles: 0.200374 torsions: N/A planes: 0.617869 non-bonded: 2.39152e-05 chiral vol: 0.0635261 rama plot: -205.772 start_pos: N/A Minimum found (iteration number 257) at -1214.71 Final Estimated RMS Z Scores: bonds: 0.113203 angles: 0.182238 torsions: N/A planes: 0.592085 non-bonded: 1.90015e-05 chiral vol: 0.0841719 rama plot: -206.401 start_pos: N/A SUCCESS TIME:: (dragged refinement): 178.076 Refinement elapsed time: 0.034 INFO:: replace_coords: 19 atoms updated. centering on A 24 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 23 and 25 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1043.31 Initial RMS Z values bonds: 0.118913 angles: 0.162802 torsions: N/A planes: 0.609722 non-bonded: 0 chiral vol: 0.18069 rama plot: -181.403 start_pos: N/A Minimum found (iteration number 362) at -1050.44 Final Estimated RMS Z Scores: bonds: 0.104395 angles: 0.184408 torsions: N/A planes: 0.48432 non-bonded: 0 chiral vol: 0.16892 rama plot: -183.995 start_pos: N/A SUCCESS TIME:: (dragged refinement): 178.651 Refinement elapsed time: 0.048 INFO:: replace_coords: 19 atoms updated. centering on A 25 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 24 and 26 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -885.685 Initial RMS Z values bonds: 0.14902 angles: 0.387862 torsions: N/A planes: 0.570398 non-bonded: 0 chiral vol: 0.197862 rama plot: -149.769 start_pos: N/A Minimum found (iteration number 332) at -891.242 Final Estimated RMS Z Scores: bonds: 0.127024 angles: 0.27829 torsions: N/A planes: 0.642456 non-bonded: 0 chiral vol: 0.187217 rama plot: -150.257 start_pos: N/A SUCCESS TIME:: (dragged refinement): 179.197 Refinement elapsed time: 0.044 INFO:: replace_coords: 18 atoms updated. centering on A 26 CA created 17 bond restraints created 18 angle restraints created 1 plane restraints created 2 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 25 and 27 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -113.684 Initial RMS Z values bonds: 0.146439 angles: 0.280373 torsions: N/A planes: 0.669593 non-bonded: 3.48753 chiral vol: 0.17165 rama plot: -150.712 start_pos: N/A Minimum found (iteration number 14) at -702.726 Final Estimated RMS Z Scores: bonds: 1.8787 angles: 1.15528 torsions: N/A planes: 0.671654 non-bonded: 0.167571 chiral vol: 0.249574 rama plot: -150.204 start_pos: N/A SUCCESS TIME:: (dragged refinement): 179.766 Refinement elapsed time: 0.056 INFO:: replace_coords: 19 atoms updated. centering on A 27 CA created 21 bond restraints created 23 angle restraints created 1 plane restraints created 2 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 26 and 28 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -850.222 Initial RMS Z values bonds: 1.72129 angles: 1.07134 torsions: N/A planes: 0.576008 non-bonded: 0.100354 chiral vol: 0.227604 rama plot: -155.66 start_pos: N/A Minimum found (iteration number 349) at -855.25 Final Estimated RMS Z Scores: bonds: 1.72024 angles: 1.07183 torsions: N/A planes: 0.488819 non-bonded: 0.10062 chiral vol: 0.161385 rama plot: -157.296 start_pos: N/A SUCCESS TIME:: (dragged refinement): 180.325 Refinement elapsed time: 0.055 INFO:: replace_coords: 22 atoms updated. centering on A 28 CA created 25 bond restraints created 29 angle restraints created 1 plane restraints created 3 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 27 and 29 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -372.379 Initial RMS Z values bonds: 1.59876 angles: 0.990148 torsions: N/A planes: 0.527094 non-bonded: 1.66078 chiral vol: 0.179819 rama plot: -186.596 start_pos: N/A Minimum found (iteration number 122) at -1041.33 Final Estimated RMS Z Scores: bonds: 1.43537 angles: 1.02654 torsions: N/A planes: 0.497081 non-bonded: 0.0804658 chiral vol: 0.26483 rama plot: -189.527 start_pos: N/A SUCCESS TIME:: (dragged refinement): 180.965 Refinement elapsed time: 0.085 INFO:: replace_coords: 25 atoms updated. centering on A 29 CA created 30 bond restraints created 36 angle restraints created 2 plane restraints created 3 chiral vol restraints created 71 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 28 and 30 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1213.49 Initial RMS Z values bonds: 1.32569 angles: 0.93152 torsions: N/A planes: 0.476006 non-bonded: 0.0613073 chiral vol: 0.274749 rama plot: -188.086 start_pos: N/A Minimum found (iteration number 345) at -1219.42 Final Estimated RMS Z Scores: bonds: 1.33358 angles: 0.936929 torsions: N/A planes: 0.430663 non-bonded: 0.0614723 chiral vol: 0.309541 rama plot: -189.971 start_pos: N/A SUCCESS TIME:: (dragged refinement): 181.614 Refinement elapsed time: 0.071 INFO:: replace_coords: 30 atoms updated. centering on A 30 CA created 24 bond restraints created 28 angle restraints created 1 plane restraints created 3 chiral vol restraints created 56 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 29 and 31 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1106.78 Initial RMS Z values bonds: 1.46975 angles: 1.08986 torsions: N/A planes: 0.488495 non-bonded: 0 chiral vol: 0.309924 rama plot: -200.135 start_pos: N/A Minimum found (iteration number 66) at -1229.65 Final Estimated RMS Z Scores: bonds: 0.143099 angles: 0.399638 torsions: N/A planes: 0.320169 non-bonded: 0 chiral vol: 0.21807 rama plot: -205.114 start_pos: N/A SUCCESS TIME:: (dragged refinement): 182.302 Refinement elapsed time: 0.075 INFO:: replace_coords: 25 atoms updated. centering on A 31 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 30 and 32 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1139.33 Initial RMS Z values bonds: 0.112477 angles: 0.398824 torsions: N/A planes: 0.684997 non-bonded: 0 chiral vol: 0.198562 rama plot: -195.68 start_pos: N/A Minimum found (iteration number 308) at -1166.3 Final Estimated RMS Z Scores: bonds: 0.127452 angles: 0.329668 torsions: N/A planes: 0.661492 non-bonded: 0 chiral vol: 0.137745 rama plot: -204.437 start_pos: N/A SUCCESS TIME:: (dragged refinement): 183.016 Refinement elapsed time: 0.117 INFO:: replace_coords: 27 atoms updated. centering on A 32 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 3 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 31 and 33 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1048.67 Initial RMS Z values bonds: 0.141567 angles: 0.371592 torsions: N/A planes: 0.606156 non-bonded: 0.103914 chiral vol: 0.144081 rama plot: -193.716 start_pos: N/A Minimum found (iteration number 247) at -1113.33 Final Estimated RMS Z Scores: bonds: 0.113306 angles: 0.432632 torsions: N/A planes: 0.640921 non-bonded: 0 chiral vol: 0.209285 rama plot: -201.067 start_pos: N/A SUCCESS TIME:: (dragged refinement): 183.737 Refinement elapsed time: 0.1 INFO:: replace_coords: 23 atoms updated. centering on A 33 CA created 18 bond restraints created 19 angle restraints created 2 plane restraints created 2 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 32 and 34 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1069.79 Initial RMS Z values bonds: 0.123078 angles: 0.514204 torsions: N/A planes: 0.729483 non-bonded: 0 chiral vol: 0.237178 rama plot: -178.997 start_pos: N/A Minimum found (iteration number 54) at -1073.1 Final Estimated RMS Z Scores: bonds: 0.125565 angles: 0.550014 torsions: N/A planes: 0.867146 non-bonded: 0 chiral vol: 0.261254 rama plot: -181.662 start_pos: N/A SUCCESS TIME:: (dragged refinement): 184.41 Refinement elapsed time: 0.068 INFO:: replace_coords: 21 atoms updated. centering on A 34 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 33 and 35 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1130.84 Initial RMS Z values bonds: 0.142693 angles: 0.396889 torsions: N/A planes: 0.840204 non-bonded: 0 chiral vol: 0.254011 rama plot: -170.472 start_pos: N/A Minimum found (iteration number 212) at -1134.19 Final Estimated RMS Z Scores: bonds: 0.15484 angles: 0.38183 torsions: N/A planes: 0.90142 non-bonded: 0 chiral vol: 0.14262 rama plot: -171.907 start_pos: N/A SUCCESS TIME:: (dragged refinement): 185.06 Refinement elapsed time: 0.03 INFO:: replace_coords: 19 atoms updated. centering on A 35 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 34 and 36 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1095.69 Initial RMS Z values bonds: 0.130898 angles: 0.365512 torsions: N/A planes: 0.837138 non-bonded: 1.10698e-05 chiral vol: 0.104502 rama plot: -172.957 start_pos: N/A Minimum found (iteration number 254) at -1096.12 Final Estimated RMS Z Scores: bonds: 0.12357 angles: 0.366157 torsions: N/A planes: 0.820717 non-bonded: 6.84703e-06 chiral vol: 0.0734992 rama plot: -173 start_pos: N/A SUCCESS TIME:: (dragged refinement): 185.768 Refinement elapsed time: 0.036 INFO:: replace_coords: 18 atoms updated. centering on A 36 CA created 23 bond restraints created 27 angle restraints created 1 plane restraints created 3 chiral vol restraints created 54 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 35 and 37 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1317.64 Initial RMS Z values bonds: 0.145729 angles: 0.362969 torsions: N/A planes: 0.857194 non-bonded: 4.19284e-06 chiral vol: 0.24301 rama plot: -181.11 start_pos: N/A Minimum found (iteration number 218) at -1318.86 Final Estimated RMS Z Scores: bonds: 0.142159 angles: 0.362268 torsions: N/A planes: 0.835273 non-bonded: 7.50387e-06 chiral vol: 0.278214 rama plot: -181.649 start_pos: N/A SUCCESS TIME:: (dragged refinement): 186.49 Refinement elapsed time: 0.038 INFO:: replace_coords: 25 atoms updated. centering on A 37 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 36 and 38 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1410.99 Initial RMS Z values bonds: 0.168173 angles: 0.484746 torsions: N/A planes: 0.889651 non-bonded: 5.70807e-06 chiral vol: 0.685047 rama plot: -192.513 start_pos: N/A Minimum found (iteration number 249) at -1416.62 Final Estimated RMS Z Scores: bonds: 0.149215 angles: 0.440912 torsions: N/A planes: 0.99721 non-bonded: 4.14557e-06 chiral vol: 0.663617 rama plot: -194.261 start_pos: N/A SUCCESS TIME:: (dragged refinement): 187.255 Refinement elapsed time: 0.048 INFO:: replace_coords: 27 atoms updated. centering on A 38 CA created 26 bond restraints created 30 angle restraints created 3 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 37 and 39 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1468.87 Initial RMS Z values bonds: 0.159987 angles: 0.48216 torsions: N/A planes: 1.08062 non-bonded: 0 chiral vol: 0.668365 rama plot: -183.861 start_pos: N/A Minimum found (iteration number 309) at -1475.52 Final Estimated RMS Z Scores: bonds: 0.159324 angles: 0.5155 torsions: N/A planes: 1.00223 non-bonded: 0 chiral vol: 0.753898 rama plot: -184.882 start_pos: N/A SUCCESS TIME:: (dragged refinement): 188.02 Refinement elapsed time: 0.059 INFO:: replace_coords: 28 atoms updated. centering on A 39 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 38 and 40 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1350.96 Initial RMS Z values bonds: 0.256482 angles: 0.891519 torsions: N/A planes: 2.29662 non-bonded: 0 chiral vol: 1.16591 rama plot: -198.95 start_pos: N/A Minimum found (iteration number 99) at -1357.96 Final Estimated RMS Z Scores: bonds: 0.218121 angles: 0.894299 torsions: N/A planes: 2.13153 non-bonded: 0 chiral vol: 1.05212 rama plot: -198.712 start_pos: N/A SUCCESS TIME:: (dragged refinement): 188.797 Refinement elapsed time: 0.1 INFO:: replace_coords: 28 atoms updated. centering on A 40 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 39 and 41 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 4407.93 Initial RMS Z values bonds: 0.270287 angles: 0.975781 torsions: N/A planes: 2.18709 non-bonded: 10.5089 chiral vol: 0.886622 rama plot: -165.76 start_pos: N/A Minimum found (iteration number 187) at -1113.75 Final Estimated RMS Z Scores: bonds: 0.260639 angles: 1.36504 torsions: N/A planes: 2.17409 non-bonded: 0.000551555 chiral vol: 1.15651 rama plot: -178.419 start_pos: N/A SUCCESS TIME:: (dragged refinement): 189.584 Refinement elapsed time: 0.114 INFO:: replace_coords: 28 atoms updated. centering on A 41 CA created 23 bond restraints created 25 angle restraints created 2 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 40 and 42 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -921.383 Initial RMS Z values bonds: 0.260991 angles: 1.41186 torsions: N/A planes: 2.22034 non-bonded: 0.000441835 chiral vol: 1.14474 rama plot: -151.251 start_pos: N/A Minimum found (iteration number 2) at -969.631 Final Estimated RMS Z Scores: bonds: 0.260458 angles: 1.17776 torsions: N/A planes: 2.39385 non-bonded: 0.000756114 chiral vol: 1.14295 rama plot: -169.423 start_pos: N/A SUCCESS TIME:: (dragged refinement): 190.318 Refinement elapsed time: 0.071 INFO:: replace_coords: 26 atoms updated. centering on A 42 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 41 and 43 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -971.057 Initial RMS Z values bonds: 0.172525 angles: 1.04919 torsions: N/A planes: 2.507 non-bonded: 7.30623e-05 chiral vol: 0.821994 rama plot: -168.736 start_pos: N/A Minimum found (iteration number 384) at -984.111 Final Estimated RMS Z Scores: bonds: 0.267091 angles: 0.860588 torsions: N/A planes: 2.48337 non-bonded: 0.000162926 chiral vol: 0.480589 rama plot: -169.668 start_pos: N/A SUCCESS TIME:: (dragged refinement): 191.073 Refinement elapsed time: 0.057 INFO:: replace_coords: 22 atoms updated. centering on A 43 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 42 and 44 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1236.52 Initial RMS Z values bonds: 0.148989 angles: 0.576034 torsions: N/A planes: 0.819505 non-bonded: 0 chiral vol: 0.275461 rama plot: -178.971 start_pos: N/A Minimum found (iteration number 250) at -1241.65 Final Estimated RMS Z Scores: bonds: 0.154674 angles: 0.577307 torsions: N/A planes: 0.893585 non-bonded: 0 chiral vol: 0.214089 rama plot: -182.116 start_pos: N/A SUCCESS TIME:: (dragged refinement): 191.744 Refinement elapsed time: 0.037 INFO:: replace_coords: 21 atoms updated. centering on A 44 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 3 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 43 and 45 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -688.927 Initial RMS Z values bonds: 0.152055 angles: 0.276011 torsions: N/A planes: 0.64141 non-bonded: 1.96958 chiral vol: 0.215211 rama plot: -191.282 start_pos: N/A Minimum found (iteration number 304) at -1193.24 Final Estimated RMS Z Scores: bonds: 1.57804 angles: 1.10415 torsions: N/A planes: 0.50615 non-bonded: 0.101786 chiral vol: 0.29735 rama plot: -191.625 start_pos: N/A SUCCESS TIME:: (dragged refinement): 192.478 Refinement elapsed time: 0.044 INFO:: replace_coords: 22 atoms updated. centering on A 45 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 44 and 46 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1146.77 Initial RMS Z values bonds: 1.57705 angles: 1.10855 torsions: N/A planes: 0.492568 non-bonded: 0.107774 chiral vol: 0.260477 rama plot: -177.347 start_pos: N/A Minimum found (iteration number 226) at -1148.9 Final Estimated RMS Z Scores: bonds: 1.57389 angles: 1.11868 torsions: N/A planes: 0.532151 non-bonded: 0.107379 chiral vol: 0.25935 rama plot: -178.357 start_pos: N/A SUCCESS TIME:: (dragged refinement): 193.222 Refinement elapsed time: 0.034 INFO:: replace_coords: 22 atoms updated. centering on A 46 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 45 and 47 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1212.02 Initial RMS Z values bonds: 1.54283 angles: 1.09727 torsions: N/A planes: 0.372367 non-bonded: 5.00024e-06 chiral vol: 0.118506 rama plot: -175.364 start_pos: N/A Minimum found (iteration number 308) at -1318.21 Final Estimated RMS Z Scores: bonds: 0.126357 angles: 0.318192 torsions: N/A planes: 0.485419 non-bonded: 1.44652e-06 chiral vol: 0.121958 rama plot: -176.803 start_pos: N/A SUCCESS TIME:: (dragged refinement): 194.001 Refinement elapsed time: 0.047 INFO:: replace_coords: 23 atoms updated. centering on A 47 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 46 and 48 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1285.91 Initial RMS Z values bonds: 0.131822 angles: 0.239778 torsions: N/A planes: 0.369628 non-bonded: 1.68467e-06 chiral vol: 0.138547 rama plot: -173.258 start_pos: N/A Minimum found (iteration number 260) at -1291.15 Final Estimated RMS Z Scores: bonds: 0.0986492 angles: 0.216119 torsions: N/A planes: 0.335888 non-bonded: 3.23774e-06 chiral vol: 0.108076 rama plot: -175.222 start_pos: N/A SUCCESS TIME:: (dragged refinement): 194.79 Refinement elapsed time: 0.042 INFO:: replace_coords: 22 atoms updated. centering on A 48 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 47 and 49 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1435.4 Initial RMS Z values bonds: 0.132789 angles: 0.202682 torsions: N/A planes: 0.34502 non-bonded: 2.85478e-06 chiral vol: 0.204005 rama plot: -175.152 start_pos: N/A Minimum found (iteration number 274) at -1437.72 Final Estimated RMS Z Scores: bonds: 0.148974 angles: 0.224817 torsions: N/A planes: 0.298373 non-bonded: 3.9316e-06 chiral vol: 0.241779 rama plot: -175.359 start_pos: N/A SUCCESS TIME:: (dragged refinement): 195.551 Refinement elapsed time: 0.05 INFO:: replace_coords: 27 atoms updated. centering on A 49 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 2 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 48 and 50 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1252.93 Initial RMS Z values bonds: 0.151966 angles: 0.214538 torsions: N/A planes: 0.63644 non-bonded: 0 chiral vol: 0.294522 rama plot: -172.086 start_pos: N/A Minimum found (iteration number 208) at -1255.07 Final Estimated RMS Z Scores: bonds: 0.165835 angles: 0.222551 torsions: N/A planes: 0.650188 non-bonded: 0 chiral vol: 0.342656 rama plot: -172.699 start_pos: N/A SUCCESS TIME:: (dragged refinement): 196.284 Refinement elapsed time: 0.037 INFO:: replace_coords: 22 atoms updated. centering on A 50 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 49 and 51 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1537.69 Initial RMS Z values bonds: 0.141088 angles: 0.223821 torsions: N/A planes: 0.685755 non-bonded: 0 chiral vol: 0.331321 rama plot: -185.51 start_pos: N/A Minimum found (iteration number 195) at -1541.08 Final Estimated RMS Z Scores: bonds: 0.135982 angles: 0.211594 torsions: N/A planes: 0.675441 non-bonded: 0 chiral vol: 0.26041 rama plot: -186.816 start_pos: N/A SUCCESS TIME:: (dragged refinement): 196.979 Refinement elapsed time: 0.04 INFO:: replace_coords: 28 atoms updated. centering on A 51 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 50 and 52 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1584.29 Initial RMS Z values bonds: 0.100769 angles: 0.255556 torsions: N/A planes: 0.742575 non-bonded: 0 chiral vol: 0.182956 rama plot: -183.806 start_pos: N/A Minimum found (iteration number 213) at -1585.17 Final Estimated RMS Z Scores: bonds: 0.118891 angles: 0.263934 torsions: N/A planes: 0.716715 non-bonded: 0 chiral vol: 0.185901 rama plot: -183.854 start_pos: N/A SUCCESS TIME:: (dragged refinement): 197.668 Refinement elapsed time: 0.046 INFO:: replace_coords: 28 atoms updated. centering on A 52 CA created 34 bond restraints created 42 angle restraints created 3 plane restraints created 3 chiral vol restraints created 82 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 51 and 53 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1809.38 Initial RMS Z values bonds: 0.120459 angles: 0.242485 torsions: N/A planes: 0.892302 non-bonded: 0 chiral vol: 0.166607 rama plot: -190.92 start_pos: N/A Minimum found (iteration number 232) at -1809.85 Final Estimated RMS Z Scores: bonds: 0.123152 angles: 0.237694 torsions: N/A planes: 0.912021 non-bonded: 0 chiral vol: 0.159945 rama plot: -191.009 start_pos: N/A SUCCESS TIME:: (dragged refinement): 198.409 Refinement elapsed time: 0.055 INFO:: replace_coords: 34 atoms updated. centering on A 53 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 52 and 54 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1602.41 Initial RMS Z values bonds: 0.146413 angles: 0.276638 torsions: N/A planes: 0.78026 non-bonded: 0 chiral vol: 0.146589 rama plot: -178.491 start_pos: N/A Minimum found (iteration number 287) at -1603.41 Final Estimated RMS Z Scores: bonds: 0.135764 angles: 0.279593 torsions: N/A planes: 0.779862 non-bonded: 0 chiral vol: 0.167796 rama plot: -178.76 start_pos: N/A SUCCESS TIME:: (dragged refinement): 199.195 Refinement elapsed time: 0.058 INFO:: replace_coords: 31 atoms updated. centering on A 54 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 53 and 55 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1602.88 Initial RMS Z values bonds: 0.162639 angles: 0.207791 torsions: N/A planes: 0.6944 non-bonded: 0 chiral vol: 0.107555 rama plot: -179.403 start_pos: N/A Minimum found (iteration number 338) at -1604.23 Final Estimated RMS Z Scores: bonds: 0.153579 angles: 0.198702 torsions: N/A planes: 0.685309 non-bonded: 0 chiral vol: 0.0921434 rama plot: -179.726 start_pos: N/A SUCCESS TIME:: (dragged refinement): 200.024 Refinement elapsed time: 0.075 INFO:: replace_coords: 31 atoms updated. centering on A 55 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 54 and 56 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1514.53 Initial RMS Z values bonds: 0.170582 angles: 0.24428 torsions: N/A planes: 1.31692 non-bonded: 0 chiral vol: 0.0850583 rama plot: -181.189 start_pos: N/A Minimum found (iteration number 198) at -1515.1 Final Estimated RMS Z Scores: bonds: 0.171563 angles: 0.255497 torsions: N/A planes: 1.31361 non-bonded: 0 chiral vol: 0.0915193 rama plot: -181.65 start_pos: N/A SUCCESS TIME:: (dragged refinement): 200.778 Refinement elapsed time: 0.044 INFO:: replace_coords: 28 atoms updated. centering on A 56 CA created 24 bond restraints created 29 angle restraints created 1 plane restraints created 4 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 55 and 57 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1493.94 Initial RMS Z values bonds: 0.196695 angles: 0.437592 torsions: N/A planes: 1.32505 non-bonded: 0 chiral vol: 0.362057 rama plot: -179.226 start_pos: N/A Minimum found (iteration number 188) at -1494.62 Final Estimated RMS Z Scores: bonds: 0.210931 angles: 0.449123 torsions: N/A planes: 1.30515 non-bonded: 0 chiral vol: 0.370981 rama plot: -179.746 start_pos: N/A SUCCESS TIME:: (dragged refinement): 201.474 Refinement elapsed time: 0.035 INFO:: replace_coords: 26 atoms updated. centering on A 57 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 56 and 58 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1330.92 Initial RMS Z values bonds: 0.217899 angles: 0.500238 torsions: N/A planes: 1.43439 non-bonded: 0.000202554 chiral vol: 0.338631 rama plot: -181.402 start_pos: N/A Minimum found (iteration number 191) at -1331.37 Final Estimated RMS Z Scores: bonds: 0.198979 angles: 0.495651 torsions: N/A planes: 1.45092 non-bonded: 0.000185255 chiral vol: 0.349418 rama plot: -181.405 start_pos: N/A SUCCESS TIME:: (dragged refinement): 202.153 Refinement elapsed time: 0.031 INFO:: replace_coords: 22 atoms updated. centering on A 58 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 57 and 59 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1268.23 Initial RMS Z values bonds: 0.193176 angles: 0.609493 torsions: N/A planes: 1.51872 non-bonded: 0.000199259 chiral vol: 0.444589 rama plot: -179.331 start_pos: N/A Minimum found (iteration number 217) at -1270.03 Final Estimated RMS Z Scores: bonds: 0.199575 angles: 0.584305 torsions: N/A planes: 1.50799 non-bonded: 0.000141433 chiral vol: 0.503257 rama plot: -179.617 start_pos: N/A SUCCESS TIME:: (dragged refinement): 202.784 Refinement elapsed time: 0.036 INFO:: replace_coords: 22 atoms updated. centering on A 59 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 5 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 58 and 60 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -588.069 Initial RMS Z values bonds: 0.160297 angles: 0.476059 torsions: N/A planes: 0.909388 non-bonded: 1.86437 chiral vol: 0.396519 rama plot: -179.942 start_pos: N/A Minimum found (iteration number 346) at -1077.66 Final Estimated RMS Z Scores: bonds: 1.56395 angles: 1.16568 torsions: N/A planes: 0.945834 non-bonded: 0.0952484 chiral vol: 0.298952 rama plot: -181.715 start_pos: N/A SUCCESS TIME:: (dragged refinement): 203.39 Refinement elapsed time: 0.053 INFO:: replace_coords: 22 atoms updated. centering on A 60 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 59 and 61 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -908.437 Initial RMS Z values bonds: 1.71066 angles: 1.28334 torsions: N/A planes: 0.765081 non-bonded: 0.143452 chiral vol: 0.370778 rama plot: -170.864 start_pos: N/A Minimum found (iteration number 287) at -910.305 Final Estimated RMS Z Scores: bonds: 1.71435 angles: 1.2651 torsions: N/A planes: 0.798992 non-bonded: 0.142895 chiral vol: 0.363939 rama plot: -171.262 start_pos: N/A SUCCESS TIME:: (dragged refinement): 203.951 Refinement elapsed time: 0.038 INFO:: replace_coords: 18 atoms updated. centering on A 61 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 60 and 62 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -877.746 Initial RMS Z values bonds: 1.80818 angles: 1.31294 torsions: N/A planes: 0.952824 non-bonded: 0 chiral vol: 0.195234 rama plot: -170.226 start_pos: N/A Minimum found (iteration number 295) at -981.83 Final Estimated RMS Z Scores: bonds: 0.123318 angles: 0.449493 torsions: N/A planes: 0.916711 non-bonded: 0 chiral vol: 0.226376 rama plot: -169.888 start_pos: N/A SUCCESS TIME:: (dragged refinement): 204.548 Refinement elapsed time: 0.034 INFO:: replace_coords: 16 atoms updated. centering on A 62 CA created 17 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 61 and 63 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1140.1 Initial RMS Z values bonds: 0.0903064 angles: 0.341062 torsions: N/A planes: 0.782912 non-bonded: 0 chiral vol: 0.219658 rama plot: -179.751 start_pos: N/A Minimum found (iteration number 217) at -1150.02 Final Estimated RMS Z Scores: bonds: 0.0976137 angles: 0.377364 torsions: N/A planes: 0.829298 non-bonded: 0 chiral vol: 0.191569 rama plot: -183.483 start_pos: N/A SUCCESS TIME:: (dragged refinement): 205.162 Refinement elapsed time: 0.031 INFO:: replace_coords: 20 atoms updated. centering on A 63 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 62 and 64 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1234.43 Initial RMS Z values bonds: 0.107932 angles: 0.307383 torsions: N/A planes: 0.797843 non-bonded: 0 chiral vol: 0.285823 rama plot: -180.464 start_pos: N/A Minimum found (iteration number 276) at -1237.61 Final Estimated RMS Z Scores: bonds: 0.103192 angles: 0.31144 torsions: N/A planes: 0.804547 non-bonded: 0 chiral vol: 0.288172 rama plot: -182.47 start_pos: N/A SUCCESS TIME:: (dragged refinement): 205.779 Refinement elapsed time: 0.047 INFO:: replace_coords: 23 atoms updated. centering on A 64 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 63 and 65 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1349.15 Initial RMS Z values bonds: 0.102495 angles: 0.30137 torsions: N/A planes: 0.766182 non-bonded: 0 chiral vol: 0.316351 rama plot: -188.726 start_pos: N/A Minimum found (iteration number 321) at -1353.47 Final Estimated RMS Z Scores: bonds: 0.111617 angles: 0.276509 torsions: N/A planes: 0.802619 non-bonded: 0 chiral vol: 0.28036 rama plot: -189.514 start_pos: N/A SUCCESS TIME:: (dragged refinement): 206.436 Refinement elapsed time: 0.059 INFO:: replace_coords: 29 atoms updated. centering on A 65 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 64 and 66 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1068.23 Initial RMS Z values bonds: 0.125506 angles: 0.319552 torsions: N/A planes: 0.6566 non-bonded: 0 chiral vol: 0.32367 rama plot: -156.775 start_pos: N/A Minimum found (iteration number 265) at -1070.31 Final Estimated RMS Z Scores: bonds: 0.128172 angles: 0.312512 torsions: N/A planes: 0.736747 non-bonded: 0 chiral vol: 0.337697 rama plot: -157.168 start_pos: N/A SUCCESS TIME:: (dragged refinement): 207.079 Refinement elapsed time: 0.04 INFO:: replace_coords: 22 atoms updated. centering on A 66 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 65 and 67 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1084.5 Initial RMS Z values bonds: 0.135467 angles: 0.430223 torsions: N/A planes: 0.956321 non-bonded: 0 chiral vol: 0.377187 rama plot: -161.927 start_pos: N/A Minimum found (iteration number 320) at -1087.48 Final Estimated RMS Z Scores: bonds: 0.14494 angles: 0.472495 torsions: N/A planes: 0.927238 non-bonded: 0 chiral vol: 0.401652 rama plot: -164.671 start_pos: N/A SUCCESS TIME:: (dragged refinement): 207.736 Refinement elapsed time: 0.049 INFO:: replace_coords: 22 atoms updated. centering on A 67 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 66 and 68 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1143.39 Initial RMS Z values bonds: 0.163898 angles: 0.447169 torsions: N/A planes: 0.892981 non-bonded: 0 chiral vol: 0.384284 rama plot: -156.872 start_pos: N/A Minimum found (iteration number 252) at -1147.28 Final Estimated RMS Z Scores: bonds: 0.135697 angles: 0.424622 torsions: N/A planes: 0.795626 non-bonded: 0 chiral vol: 0.359697 rama plot: -156.814 start_pos: N/A SUCCESS TIME:: (dragged refinement): 208.402 Refinement elapsed time: 0.039 INFO:: replace_coords: 22 atoms updated. centering on A 68 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 67 and 69 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1461.48 Initial RMS Z values bonds: 0.149572 angles: 0.387105 torsions: N/A planes: 1.12556 non-bonded: 0 chiral vol: 0.313636 rama plot: -173.831 start_pos: N/A Minimum found (iteration number 191) at -1461.89 Final Estimated RMS Z Scores: bonds: 0.136312 angles: 0.391239 torsions: N/A planes: 1.12393 non-bonded: 0 chiral vol: 0.317104 rama plot: -174.152 start_pos: N/A SUCCESS TIME:: (dragged refinement): 209.089 Refinement elapsed time: 0.038 INFO:: replace_coords: 29 atoms updated. centering on A 69 CA created 27 bond restraints created 30 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 68 and 70 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1540.71 Initial RMS Z values bonds: 0.183976 angles: 0.397856 torsions: N/A planes: 1.12939 non-bonded: 0.0001387 chiral vol: 0.220322 rama plot: -179.089 start_pos: N/A Minimum found (iteration number 182) at -1541.18 Final Estimated RMS Z Scores: bonds: 0.169897 angles: 0.361182 torsions: N/A planes: 1.1533 non-bonded: 0.000166367 chiral vol: 0.216882 rama plot: -178.983 start_pos: N/A SUCCESS TIME:: (dragged refinement): 209.838 Refinement elapsed time: 0.038 INFO:: replace_coords: 30 atoms updated. centering on A 70 CA created 24 bond restraints created 27 angle restraints created 1 plane restraints created 5 chiral vol restraints created 57 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 69 and 71 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 3 plane links initial distortion_score: -1293.66 Initial RMS Z values bonds: 0.204214 angles: 0.411606 torsions: N/A planes: 1.11628 non-bonded: 0.000172675 chiral vol: 0.194967 rama plot: -178.639 start_pos: N/A Minimum found (iteration number 308) at -1297.89 Final Estimated RMS Z Scores: bonds: 0.150798 angles: 0.377249 torsions: N/A planes: 1.05655 non-bonded: 0.000173111 chiral vol: 0.19762 rama plot: -178.544 start_pos: N/A SUCCESS TIME:: (dragged refinement): 210.693 Refinement elapsed time: 0.05 INFO:: replace_coords: 27 atoms updated. centering on A 71 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 4 chiral vol restraints created 39 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 70 and 72 of chain A Link restraints: 1 bond links 3 angle links 3 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 2020.04 Initial RMS Z values bonds: 0.17407 angles: 0.404896 torsions: N/A planes: 1.14114 non-bonded: 10.4337 chiral vol: 0.214226 rama plot: -183.129 start_pos: N/A Minimum found (iteration number 2) at -856.408 Final Estimated RMS Z Scores: bonds: 0.284842 angles: 0.497799 torsions: N/A planes: 1.97636 non-bonded: 0.00114915 chiral vol: 0.226532 rama plot: -183.134 start_pos: N/A SUCCESS TIME:: (dragged refinement): 211.527 Refinement elapsed time: 0.049 INFO:: replace_coords: 20 atoms updated. centering on A 72 CA created 13 bond restraints created 12 angle restraints created 0 plane restraints created 2 chiral vol restraints created 27 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 71 and 73 of chain A Link restraints: 1 bond links 3 angle links 3 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -727.2 Initial RMS Z values bonds: 0.270223 angles: 0.410608 torsions: N/A planes: 1.73392 non-bonded: 0.00154138 chiral vol: 0.245926 rama plot: -165.106 start_pos: N/A Minimum found (iteration number 273) at -741.021 Final Estimated RMS Z Scores: bonds: 0.249353 angles: 0.651245 torsions: N/A planes: 1.10551 non-bonded: 0.00092461 chiral vol: 0.224904 rama plot: -175.626 start_pos: N/A SUCCESS TIME:: (dragged refinement): 212.33 Refinement elapsed time: 0.029 INFO:: replace_coords: 16 atoms updated. centering on A 73 CA created 14 bond restraints created 13 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 72 and 74 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 3 plane links initial distortion_score: -929.006 Initial RMS Z values bonds: 0.186964 angles: 0.604948 torsions: N/A planes: 1.06524 non-bonded: 0 chiral vol: 0.469592 rama plot: -190.472 start_pos: N/A Minimum found (iteration number 13) at -956.839 Final Estimated RMS Z Scores: bonds: 0.159465 angles: 0.305911 torsions: N/A planes: 0.63645 non-bonded: 0 chiral vol: 0.377838 rama plot: -196.252 start_pos: N/A SUCCESS TIME:: (dragged refinement): 213.095 Refinement elapsed time: 0.046 INFO:: replace_coords: 17 atoms updated. centering on A 74 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 73 and 75 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1168.64 Initial RMS Z values bonds: 0.139819 angles: 0.312726 torsions: N/A planes: 0.610377 non-bonded: 0 chiral vol: 0.283005 rama plot: -189.256 start_pos: N/A Minimum found (iteration number 268) at -1172.67 Final Estimated RMS Z Scores: bonds: 0.149305 angles: 0.312098 torsions: N/A planes: 0.53893 non-bonded: 0 chiral vol: 0.358925 rama plot: -190.921 start_pos: N/A SUCCESS TIME:: (dragged refinement): 213.759 Refinement elapsed time: 0.035 INFO:: replace_coords: 18 atoms updated. centering on A 75 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 74 and 76 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1254.47 Initial RMS Z values bonds: 0.161177 angles: 0.298288 torsions: N/A planes: 0.685988 non-bonded: 0 chiral vol: 0.345453 rama plot: -190.165 start_pos: N/A Minimum found (iteration number 195) at -1259.08 Final Estimated RMS Z Scores: bonds: 0.16162 angles: 0.311964 torsions: N/A planes: 0.659666 non-bonded: 0 chiral vol: 0.343333 rama plot: -192.235 start_pos: N/A SUCCESS TIME:: (dragged refinement): 214.472 Refinement elapsed time: 0.031 INFO:: replace_coords: 21 atoms updated. centering on A 76 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 75 and 77 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1194.5 Initial RMS Z values bonds: 0.154979 angles: 0.375016 torsions: N/A planes: 0.583578 non-bonded: 0 chiral vol: 0.297024 rama plot: -169.534 start_pos: N/A Minimum found (iteration number 270) at -1199.1 Final Estimated RMS Z Scores: bonds: 0.150496 angles: 0.382762 torsions: N/A planes: 0.556797 non-bonded: 0 chiral vol: 0.343134 rama plot: -170.038 start_pos: N/A SUCCESS TIME:: (dragged refinement): 215.235 Refinement elapsed time: 0.042 INFO:: replace_coords: 21 atoms updated. centering on A 77 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 76 and 78 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1370.07 Initial RMS Z values bonds: 0.157908 angles: 0.370876 torsions: N/A planes: 0.485617 non-bonded: 0 chiral vol: 0.337589 rama plot: -159.124 start_pos: N/A Minimum found (iteration number 386) at -1374.89 Final Estimated RMS Z Scores: bonds: 0.158384 angles: 0.35348 torsions: N/A planes: 0.42049 non-bonded: 0 chiral vol: 0.263759 rama plot: -160.964 start_pos: N/A SUCCESS TIME:: (dragged refinement): 216.074 Refinement elapsed time: 0.066 INFO:: replace_coords: 25 atoms updated. centering on A 78 CA created 23 bond restraints created 26 angle restraints created 3 plane restraints created 3 chiral vol restraints created 55 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 77 and 79 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1482.2 Initial RMS Z values bonds: 0.183336 angles: 0.333399 torsions: N/A planes: 0.420447 non-bonded: 0 chiral vol: 0.140314 rama plot: -159.692 start_pos: N/A Minimum found (iteration number 270) at -1486.41 Final Estimated RMS Z Scores: bonds: 0.175625 angles: 0.312438 torsions: N/A planes: 0.531785 non-bonded: 0 chiral vol: 0.153591 rama plot: -160.277 start_pos: N/A SUCCESS TIME:: (dragged refinement): 216.903 Refinement elapsed time: 0.051 INFO:: replace_coords: 26 atoms updated. centering on A 79 CA created 27 bond restraints created 32 angle restraints created 3 plane restraints created 3 chiral vol restraints created 65 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 78 and 80 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1687.8 Initial RMS Z values bonds: 0.180238 angles: 0.274979 torsions: N/A planes: 0.3222 non-bonded: 0 chiral vol: 0.0393505 rama plot: -168.042 start_pos: N/A Minimum found (iteration number 169) at -1688.81 Final Estimated RMS Z Scores: bonds: 0.164606 angles: 0.276157 torsions: N/A planes: 0.290177 non-bonded: 0 chiral vol: 0.055993 rama plot: -168.575 start_pos: N/A SUCCESS TIME:: (dragged refinement): 217.744 Refinement elapsed time: 0.039 INFO:: replace_coords: 29 atoms updated. centering on A 80 CA created 31 bond restraints created 38 angle restraints created 3 plane restraints created 3 chiral vol restraints created 75 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 79 and 81 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1726.3 Initial RMS Z values bonds: 0.158324 angles: 0.174724 torsions: N/A planes: 0.679115 non-bonded: 0 chiral vol: 0.115305 rama plot: -179.012 start_pos: N/A Minimum found (iteration number 191) at -1727.7 Final Estimated RMS Z Scores: bonds: 0.156977 angles: 0.173491 torsions: N/A planes: 0.75009 non-bonded: 0 chiral vol: 0.12286 rama plot: -179.362 start_pos: N/A SUCCESS TIME:: (dragged refinement): 218.56 Refinement elapsed time: 0.043 INFO:: replace_coords: 32 atoms updated. centering on A 81 CA created 30 bond restraints created 37 angle restraints created 2 plane restraints created 4 chiral vol restraints created 73 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 80 and 82 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1643.79 Initial RMS Z values bonds: 0.126938 angles: 0.168808 torsions: N/A planes: 0.851671 non-bonded: 0 chiral vol: 0.114639 rama plot: -180.209 start_pos: N/A Minimum found (iteration number 197) at -1645.96 Final Estimated RMS Z Scores: bonds: 0.135416 angles: 0.174255 torsions: N/A planes: 0.843835 non-bonded: 0 chiral vol: 0.0933729 rama plot: -180.968 start_pos: N/A SUCCESS TIME:: (dragged refinement): 219.347 Refinement elapsed time: 0.041 INFO:: replace_coords: 31 atoms updated. centering on A 82 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 81 and 83 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1349.62 Initial RMS Z values bonds: 0.131407 angles: 0.188211 torsions: N/A planes: 0.977783 non-bonded: 0 chiral vol: 0.104464 rama plot: -177.543 start_pos: N/A Minimum found (iteration number 206) at -1352.75 Final Estimated RMS Z Scores: bonds: 0.118807 angles: 0.176161 torsions: N/A planes: 0.904981 non-bonded: 0 chiral vol: 0.123051 rama plot: -178.244 start_pos: N/A SUCCESS TIME:: (dragged refinement): 220.07 Refinement elapsed time: 0.037 INFO:: replace_coords: 23 atoms updated. centering on A 83 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 82 and 84 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1200.01 Initial RMS Z values bonds: 0.160217 angles: 0.366326 torsions: N/A planes: 0.897876 non-bonded: 0 chiral vol: 0.61812 rama plot: -161.985 start_pos: N/A Minimum found (iteration number 187) at -1205.46 Final Estimated RMS Z Scores: bonds: 0.162253 angles: 0.392552 torsions: N/A planes: 0.890931 non-bonded: 0 chiral vol: 0.619931 rama plot: -164.666 start_pos: N/A SUCCESS TIME:: (dragged refinement): 220.704 Refinement elapsed time: 0.028 INFO:: replace_coords: 19 atoms updated. centering on A 84 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 2 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 83 and 85 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1142.81 Initial RMS Z values bonds: 0.160366 angles: 0.418604 torsions: N/A planes: 0.781108 non-bonded: 0 chiral vol: 0.880527 rama plot: -150.987 start_pos: N/A Minimum found (iteration number 347) at -1151.28 Final Estimated RMS Z Scores: bonds: 0.149739 angles: 0.396836 torsions: N/A planes: 0.806929 non-bonded: 0 chiral vol: 0.857567 rama plot: -153.479 start_pos: N/A SUCCESS TIME:: (dragged refinement): 221.352 Refinement elapsed time: 0.052 INFO:: replace_coords: 22 atoms updated. centering on A 85 CA created 29 bond restraints created 35 angle restraints created 3 plane restraints created 3 chiral vol restraints created 70 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 84 and 86 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1325.79 Initial RMS Z values bonds: 0.154289 angles: 0.467247 torsions: N/A planes: 0.741488 non-bonded: 0.000214828 chiral vol: 0.774983 rama plot: -147.955 start_pos: N/A Minimum found (iteration number 366) at -1330.74 Final Estimated RMS Z Scores: bonds: 0.148512 angles: 0.446469 torsions: N/A planes: 0.784876 non-bonded: 0 chiral vol: 0.775576 rama plot: -148.138 start_pos: N/A SUCCESS TIME:: (dragged refinement): 222.099 Refinement elapsed time: 0.078 INFO:: replace_coords: 30 atoms updated. centering on A 86 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 85 and 87 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1240.66 Initial RMS Z values bonds: 0.12567 angles: 0.400724 torsions: N/A planes: 0.776988 non-bonded: 0 chiral vol: 0.496706 rama plot: -170.239 start_pos: N/A Minimum found (iteration number 2) at -1252.37 Final Estimated RMS Z Scores: bonds: 0.13951 angles: 0.42524 torsions: N/A planes: 0.762417 non-bonded: 0 chiral vol: 0.496662 rama plot: -176.244 start_pos: N/A SUCCESS TIME:: (dragged refinement): 222.831 Refinement elapsed time: 0.077 INFO:: replace_coords: 27 atoms updated. centering on A 87 CA created 22 bond restraints created 26 angle restraints created 1 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 86 and 88 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1237.04 Initial RMS Z values bonds: 0.12509 angles: 0.403124 torsions: N/A planes: 0.779276 non-bonded: 0 chiral vol: 0.296087 rama plot: -183.86 start_pos: N/A Minimum found (iteration number 269) at -1239.62 Final Estimated RMS Z Scores: bonds: 0.13268 angles: 0.410471 torsions: N/A planes: 0.712177 non-bonded: 0 chiral vol: 0.304649 rama plot: -183.788 start_pos: N/A SUCCESS TIME:: (dragged refinement): 223.46 Refinement elapsed time: 0.042 INFO:: replace_coords: 24 atoms updated. centering on A 88 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 87 and 89 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1099.24 Initial RMS Z values bonds: 0.13991 angles: 0.319805 torsions: N/A planes: 0.564947 non-bonded: 0.000257585 chiral vol: 0.259757 rama plot: -190.471 start_pos: N/A Minimum found (iteration number 197) at -1099.83 Final Estimated RMS Z Scores: bonds: 0.139508 angles: 0.322362 torsions: N/A planes: 0.613462 non-bonded: 0.00022535 chiral vol: 0.258083 rama plot: -190.882 start_pos: N/A SUCCESS TIME:: (dragged refinement): 224.107 Refinement elapsed time: 0.087 INFO:: replace_coords: 23 atoms updated. centering on A 89 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 4 chiral vol restraints created 52 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 88 and 90 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1157.82 Initial RMS Z values bonds: 0.13615 angles: 0.245711 torsions: N/A planes: 0.614082 non-bonded: 0.000182591 chiral vol: 0.23969 rama plot: -177.838 start_pos: N/A Minimum found (iteration number 387) at -1159.74 Final Estimated RMS Z Scores: bonds: 0.126402 angles: 0.234457 torsions: N/A planes: 0.614511 non-bonded: 0.000211847 chiral vol: 0.240701 rama plot: -178.095 start_pos: N/A SUCCESS TIME:: (dragged refinement): 224.863 Refinement elapsed time: 0.126 INFO:: replace_coords: 24 atoms updated. centering on A 90 CA created 23 bond restraints created 26 angle restraints created 1 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 89 and 91 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1190.51 Initial RMS Z values bonds: 0.140963 angles: 0.330319 torsions: N/A planes: 0.585581 non-bonded: 0.000200535 chiral vol: 0.393627 rama plot: -178.109 start_pos: N/A Minimum found (iteration number 392) at -1192.29 Final Estimated RMS Z Scores: bonds: 0.145426 angles: 0.346102 torsions: N/A planes: 0.667669 non-bonded: 0.000196673 chiral vol: 0.412308 rama plot: -179.41 start_pos: N/A SUCCESS TIME:: (dragged refinement): 225.574 Refinement elapsed time: 0.066 INFO:: replace_coords: 25 atoms updated. centering on A 91 CA created 19 bond restraints created 21 angle restraints created 0 plane restraints created 4 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 90 and 92 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1292.68 Initial RMS Z values bonds: 0.124976 angles: 0.327572 torsions: N/A planes: 0.716163 non-bonded: 0 chiral vol: 0.29215 rama plot: -178.55 start_pos: N/A Minimum found (iteration number 320) at -1294.47 Final Estimated RMS Z Scores: bonds: 0.127548 angles: 0.339807 torsions: N/A planes: 0.74002 non-bonded: 2.28166e-06 chiral vol: 0.298144 rama plot: -180.017 start_pos: N/A SUCCESS TIME:: (dragged refinement): 226.317 Refinement elapsed time: 0.048 INFO:: replace_coords: 22 atoms updated. centering on A 92 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 91 and 93 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -1063.33 Initial RMS Z values bonds: 0.122396 angles: 0.323136 torsions: N/A planes: 0.615002 non-bonded: 1.96411e-06 chiral vol: 0.287112 rama plot: -176.869 start_pos: N/A Minimum found (iteration number 372) at -1065.06 Final Estimated RMS Z Scores: bonds: 0.112929 angles: 0.290626 torsions: N/A planes: 0.479058 non-bonded: 0 chiral vol: 0.254848 rama plot: -174.709 start_pos: N/A SUCCESS TIME:: (dragged refinement): 227.141 Refinement elapsed time: 0.051 INFO:: replace_coords: 24 atoms updated. centering on A 93 CA created 14 bond restraints created 16 angle restraints created 1 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 92 and 93 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -648.656 Initial RMS Z values bonds: 0.0904483 angles: 0.133906 torsions: N/A planes: 0.12888 non-bonded: 0 chiral vol: 0.0740678 rama plot: N/A start_pos: N/A Minimum found (iteration number 134) at -648.898 Final Estimated RMS Z Scores: bonds: 0.0871315 angles: 0.113379 torsions: N/A planes: 0.169464 non-bonded: 0 chiral vol: 0.0408019 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 227.876 Refinement elapsed time: 0.013 INFO:: replace_coords: 16 atoms updated. There are 96 residues in chain B centering on B 1 CA created 13 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain B Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -372.832 Initial RMS Z values bonds: 0.150409 angles: 0.368153 torsions: N/A planes: 0.987728 non-bonded: 0 chiral vol: 0.288691 rama plot: N/A start_pos: N/A Minimum found (iteration number 247) at -377.346 Final Estimated RMS Z Scores: bonds: 0.109906 angles: 0.304537 torsions: N/A planes: 1.01752 non-bonded: 0 chiral vol: 0.249981 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 228.446 Refinement elapsed time: 0.021 INFO:: replace_coords: 15 atoms updated. centering on B 2 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 1 and 3 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -677.549 Initial RMS Z values bonds: 0.139967 angles: 0.289481 torsions: N/A planes: 0.872413 non-bonded: 0 chiral vol: 0.292709 rama plot: -173.017 start_pos: N/A Minimum found (iteration number 369) at -684.742 Final Estimated RMS Z Scores: bonds: 0.156664 angles: 0.328708 torsions: N/A planes: 1.03642 non-bonded: 0 chiral vol: 0.30374 rama plot: -178.767 start_pos: N/A SUCCESS TIME:: (dragged refinement): 229.144 Refinement elapsed time: 0.088 INFO:: replace_coords: 21 atoms updated. centering on B 3 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 2 and 4 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -890.363 Initial RMS Z values bonds: 0.192954 angles: 0.364413 torsions: N/A planes: 1.0291 non-bonded: 0 chiral vol: 0.338495 rama plot: -159.665 start_pos: N/A Minimum found (iteration number 308) at -915.088 Final Estimated RMS Z Scores: bonds: 0.223841 angles: 0.391237 torsions: N/A planes: 0.91693 non-bonded: 0 chiral vol: 0.37798 rama plot: -170.764 start_pos: N/A SUCCESS TIME:: (dragged refinement): 229.791 Refinement elapsed time: 0.038 INFO:: replace_coords: 17 atoms updated. centering on B 4 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 3 and 5 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -920.403 Initial RMS Z values bonds: 0.222034 angles: 0.319503 torsions: N/A planes: 0.662878 non-bonded: 0 chiral vol: 0.274011 rama plot: -170.298 start_pos: N/A Minimum found (iteration number 193) at -921.302 Final Estimated RMS Z Scores: bonds: 0.188425 angles: 0.284813 torsions: N/A planes: 0.727671 non-bonded: 0 chiral vol: 0.24974 rama plot: -169.696 start_pos: N/A SUCCESS TIME:: (dragged refinement): 230.442 Refinement elapsed time: 0.025 INFO:: replace_coords: 17 atoms updated. centering on B 5 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 4 and 6 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -942.012 Initial RMS Z values bonds: 0.180835 angles: 0.294154 torsions: N/A planes: 0.668207 non-bonded: 0 chiral vol: 0.14498 rama plot: -157.013 start_pos: N/A Minimum found (iteration number 231) at -943.224 Final Estimated RMS Z Scores: bonds: 0.156567 angles: 0.280386 torsions: N/A planes: 0.56623 non-bonded: 0 chiral vol: 0.139069 rama plot: -156.822 start_pos: N/A SUCCESS TIME:: (dragged refinement): 231.1 Refinement elapsed time: 0.031 INFO:: replace_coords: 18 atoms updated. centering on B 6 CA created 17 bond restraints created 19 angle restraints created 0 plane restraints created 4 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 5 and 7 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1252.37 Initial RMS Z values bonds: 0.126965 angles: 0.234481 torsions: N/A planes: 0.588721 non-bonded: 0 chiral vol: 0.120936 rama plot: -181.066 start_pos: N/A Minimum found (iteration number 224) at -1253.88 Final Estimated RMS Z Scores: bonds: 0.13159 angles: 0.213117 torsions: N/A planes: 0.571988 non-bonded: 0 chiral vol: 0.12673 rama plot: -181.478 start_pos: N/A SUCCESS TIME:: (dragged refinement): 231.797 Refinement elapsed time: 0.032 INFO:: replace_coords: 20 atoms updated. centering on B 7 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 6 and 8 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1367.88 Initial RMS Z values bonds: 0.11583 angles: 0.222714 torsions: N/A planes: 0.501821 non-bonded: 0 chiral vol: 0.0752957 rama plot: -193.422 start_pos: N/A Minimum found (iteration number 258) at -1373.68 Final Estimated RMS Z Scores: bonds: 0.168487 angles: 0.265806 torsions: N/A planes: 0.392286 non-bonded: 0 chiral vol: 0.161891 rama plot: -195.675 start_pos: N/A SUCCESS TIME:: (dragged refinement): 232.448 Refinement elapsed time: 0.036 INFO:: replace_coords: 21 atoms updated. centering on B 8 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 3 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 7 and 9 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1414.46 Initial RMS Z values bonds: 0.175968 angles: 0.377429 torsions: N/A planes: 0.388453 non-bonded: 0 chiral vol: 0.188432 rama plot: -204.957 start_pos: N/A Minimum found (iteration number 243) at -1418.46 Final Estimated RMS Z Scores: bonds: 0.147326 angles: 0.320772 torsions: N/A planes: 0.476267 non-bonded: 0 chiral vol: 0.107678 rama plot: -206.372 start_pos: N/A SUCCESS TIME:: (dragged refinement): 233.08 Refinement elapsed time: 0.035 INFO:: replace_coords: 20 atoms updated. centering on B 9 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 8 and 10 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1230.01 Initial RMS Z values bonds: 0.147716 angles: 0.371464 torsions: N/A planes: 0.701332 non-bonded: 0 chiral vol: 0.213068 rama plot: -215.984 start_pos: N/A Minimum found (iteration number 256) at -1233.84 Final Estimated RMS Z Scores: bonds: 0.183267 angles: 0.374839 torsions: N/A planes: 0.735203 non-bonded: 0 chiral vol: 0.223588 rama plot: -217.394 start_pos: N/A SUCCESS TIME:: (dragged refinement): 233.674 Refinement elapsed time: 0.034 INFO:: replace_coords: 19 atoms updated. centering on B 10 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 9 and 11 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1190.66 Initial RMS Z values bonds: 0.21086 angles: 0.450221 torsions: N/A planes: 0.901458 non-bonded: 0 chiral vol: 0.331705 rama plot: -200.895 start_pos: N/A Minimum found (iteration number 304) at -1202.51 Final Estimated RMS Z Scores: bonds: 0.189241 angles: 0.436818 torsions: N/A planes: 0.628369 non-bonded: 0 chiral vol: 0.290053 rama plot: -204.315 start_pos: N/A SUCCESS TIME:: (dragged refinement): 234.331 Refinement elapsed time: 0.041 INFO:: replace_coords: 19 atoms updated. centering on B 11 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 10 and 12 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -546.483 Initial RMS Z values bonds: 0.181225 angles: 0.462299 torsions: N/A planes: 0.885447 non-bonded: 2.2505 chiral vol: 0.310709 rama plot: -186.992 start_pos: N/A Minimum found (iteration number 326) at -1041.4 Final Estimated RMS Z Scores: bonds: 1.64311 angles: 1.20701 torsions: N/A planes: 1.03913 non-bonded: 0.118682 chiral vol: 0.350607 rama plot: -190.52 start_pos: N/A SUCCESS TIME:: (dragged refinement): 235.013 Refinement elapsed time: 0.044 INFO:: replace_coords: 20 atoms updated. centering on B 12 CA created 21 bond restraints created 24 angle restraints created 0 plane restraints created 3 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 11 and 13 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -376.672 Initial RMS Z values bonds: 1.54447 angles: 1.16586 torsions: N/A planes: 1.11486 non-bonded: 2.41546 chiral vol: 0.305657 rama plot: -183.148 start_pos: N/A Minimum found (iteration number 63) at -986.037 Final Estimated RMS Z Scores: bonds: 2.15343 angles: 1.56288 torsions: N/A planes: 0.952514 non-bonded: 0.205813 chiral vol: 0.356006 rama plot: -186.072 start_pos: N/A SUCCESS TIME:: (dragged refinement): 235.725 Refinement elapsed time: 0.07 INFO:: replace_coords: 22 atoms updated. centering on B 13 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 3 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 12 and 14 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1088.78 Initial RMS Z values bonds: 2.10956 angles: 1.52932 torsions: N/A planes: 0.732531 non-bonded: 0.0832648 chiral vol: 0.255683 rama plot: -186.403 start_pos: N/A Minimum found (iteration number 362) at -1215.52 Final Estimated RMS Z Scores: bonds: 1.50715 angles: 1.10262 torsions: N/A planes: 0.841606 non-bonded: 0.0829783 chiral vol: 0.219896 rama plot: -195.591 start_pos: N/A SUCCESS TIME:: (dragged refinement): 236.37 Refinement elapsed time: 0.06 INFO:: replace_coords: 23 atoms updated. centering on B 14 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 13 and 15 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1253.97 Initial RMS Z values bonds: 1.60187 angles: 1.13261 torsions: N/A planes: 0.787476 non-bonded: 0 chiral vol: 0.217742 rama plot: -205.656 start_pos: N/A Minimum found (iteration number 2) at -1370.57 Final Estimated RMS Z Scores: bonds: 0.158853 angles: 0.393088 torsions: N/A planes: 0.82227 non-bonded: 0 chiral vol: 0.142487 rama plot: -211.142 start_pos: N/A SUCCESS TIME:: (dragged refinement): 237.04 Refinement elapsed time: 0.057 INFO:: replace_coords: 21 atoms updated. centering on B 15 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 14 and 16 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1387.44 Initial RMS Z values bonds: 0.133813 angles: 0.267236 torsions: N/A planes: 0.544811 non-bonded: 0 chiral vol: 0.130749 rama plot: -215.201 start_pos: N/A Minimum found (iteration number 295) at -1390.74 Final Estimated RMS Z Scores: bonds: 0.13053 angles: 0.308019 torsions: N/A planes: 0.607348 non-bonded: 2.18024e-06 chiral vol: 0.191102 rama plot: -216.846 start_pos: N/A SUCCESS TIME:: (dragged refinement): 237.706 Refinement elapsed time: 0.043 INFO:: replace_coords: 21 atoms updated. centering on B 16 CA created 17 bond restraints created 19 angle restraints created 1 plane restraints created 4 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 15 and 17 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1361.86 Initial RMS Z values bonds: 0.154164 angles: 0.322293 torsions: N/A planes: 0.486494 non-bonded: 2.04398e-06 chiral vol: 0.292697 rama plot: -219.609 start_pos: N/A Minimum found (iteration number 301) at -1365.41 Final Estimated RMS Z Scores: bonds: 0.16761 angles: 0.322804 torsions: N/A planes: 0.484379 non-bonded: 0 chiral vol: 0.277823 rama plot: -220.89 start_pos: N/A SUCCESS TIME:: (dragged refinement): 238.282 Refinement elapsed time: 0.042 INFO:: replace_coords: 20 atoms updated. centering on B 17 CA created 19 bond restraints created 22 angle restraints created 1 plane restraints created 5 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 16 and 18 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1438.21 Initial RMS Z values bonds: 0.158225 angles: 0.296223 torsions: N/A planes: 0.461049 non-bonded: 0 chiral vol: 0.223209 rama plot: -220.614 start_pos: N/A Minimum found (iteration number 213) at -1439.34 Final Estimated RMS Z Scores: bonds: 0.153541 angles: 0.304017 torsions: N/A planes: 0.410733 non-bonded: 0 chiral vol: 0.233538 rama plot: -220.719 start_pos: N/A SUCCESS TIME:: (dragged refinement): 238.853 Refinement elapsed time: 0.034 INFO:: replace_coords: 22 atoms updated. centering on B 18 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 17 and 19 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1423.48 Initial RMS Z values bonds: 0.134432 angles: 0.288903 torsions: N/A planes: 0.28803 non-bonded: 0 chiral vol: 0.254798 rama plot: -220.73 start_pos: N/A Minimum found (iteration number 218) at -1424.08 Final Estimated RMS Z Scores: bonds: 0.130261 angles: 0.294005 torsions: N/A planes: 0.262123 non-bonded: 0 chiral vol: 0.261901 rama plot: -220.921 start_pos: N/A SUCCESS TIME:: (dragged refinement): 239.475 Refinement elapsed time: 0.035 INFO:: replace_coords: 23 atoms updated. centering on B 19 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 18 and 20 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1376.82 Initial RMS Z values bonds: 0.114614 angles: 0.165028 torsions: N/A planes: 0.352806 non-bonded: 0 chiral vol: 0.147208 rama plot: -221.123 start_pos: N/A Minimum found (iteration number 273) at -1377.8 Final Estimated RMS Z Scores: bonds: 0.10999 angles: 0.162833 torsions: N/A planes: 0.353317 non-bonded: 0 chiral vol: 0.125674 rama plot: -221.407 start_pos: N/A SUCCESS TIME:: (dragged refinement): 240.054 Refinement elapsed time: 0.041 INFO:: replace_coords: 23 atoms updated. centering on B 20 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 19 and 21 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1322.35 Initial RMS Z values bonds: 0.10318 angles: 0.196736 torsions: N/A planes: 0.352664 non-bonded: 0 chiral vol: 0.167003 rama plot: -221.228 start_pos: N/A Minimum found (iteration number 238) at -1322.99 Final Estimated RMS Z Scores: bonds: 0.102214 angles: 0.191288 torsions: N/A planes: 0.332392 non-bonded: 0 chiral vol: 0.157249 rama plot: -221.409 start_pos: N/A SUCCESS TIME:: (dragged refinement): 240.57 Refinement elapsed time: 0.04 INFO:: replace_coords: 24 atoms updated. centering on B 21 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 20 and 22 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1324.43 Initial RMS Z values bonds: 0.102098 angles: 0.173375 torsions: N/A planes: 0.339917 non-bonded: 6.89453e-07 chiral vol: 0.130857 rama plot: -221.417 start_pos: N/A Minimum found (iteration number 231) at -1324.77 Final Estimated RMS Z Scores: bonds: 0.107809 angles: 0.17308 torsions: N/A planes: 0.327495 non-bonded: 1.36802e-07 chiral vol: 0.138294 rama plot: -221.438 start_pos: N/A SUCCESS TIME:: (dragged refinement): 241.138 Refinement elapsed time: 0.038 INFO:: replace_coords: 24 atoms updated. centering on B 22 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 4 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 21 and 23 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1216.48 Initial RMS Z values bonds: 0.103435 angles: 0.166379 torsions: N/A planes: 0.320129 non-bonded: 1.78681e-07 chiral vol: 0.0986023 rama plot: -221.303 start_pos: N/A Minimum found (iteration number 209) at -1216.98 Final Estimated RMS Z Scores: bonds: 0.101251 angles: 0.162048 torsions: N/A planes: 0.293629 non-bonded: 3.16858e-07 chiral vol: 0.0876863 rama plot: -221.43 start_pos: N/A SUCCESS TIME:: (dragged refinement): 241.714 Refinement elapsed time: 0.031 INFO:: replace_coords: 21 atoms updated. centering on B 23 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 4 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 22 and 24 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1109.01 Initial RMS Z values bonds: 0.100631 angles: 0.144419 torsions: N/A planes: 0.442788 non-bonded: 3.91413e-07 chiral vol: 0.0835025 rama plot: -206.774 start_pos: N/A Minimum found (iteration number 341) at -1111.16 Final Estimated RMS Z Scores: bonds: 0.106157 angles: 0.143688 torsions: N/A planes: 0.502632 non-bonded: 1.27448e-06 chiral vol: 0.102068 rama plot: -207.108 start_pos: N/A SUCCESS TIME:: (dragged refinement): 242.223 Refinement elapsed time: 0.043 INFO:: replace_coords: 19 atoms updated. centering on B 24 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 23 and 25 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -992.269 Initial RMS Z values bonds: 0.12969 angles: 0.231342 torsions: N/A planes: 0.544474 non-bonded: 0 chiral vol: 0.320365 rama plot: -180.838 start_pos: N/A Minimum found (iteration number 330) at -1002.29 Final Estimated RMS Z Scores: bonds: 0.126138 angles: 0.224502 torsions: N/A planes: 0.414046 non-bonded: 0 chiral vol: 0.287706 rama plot: -184.853 start_pos: N/A SUCCESS TIME:: (dragged refinement): 242.724 Refinement elapsed time: 0.044 INFO:: replace_coords: 19 atoms updated. centering on B 25 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 24 and 26 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -881.814 Initial RMS Z values bonds: 0.154846 angles: 0.420786 torsions: N/A planes: 0.560437 non-bonded: 0 chiral vol: 0.350272 rama plot: -150.697 start_pos: N/A Minimum found (iteration number 284) at -885.836 Final Estimated RMS Z Scores: bonds: 0.109741 angles: 0.349103 torsions: N/A planes: 0.651651 non-bonded: 0 chiral vol: 0.332053 rama plot: -150.889 start_pos: N/A SUCCESS TIME:: (dragged refinement): 243.302 Refinement elapsed time: 0.038 INFO:: replace_coords: 18 atoms updated. centering on B 26 CA created 17 bond restraints created 18 angle restraints created 1 plane restraints created 2 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 25 and 27 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -152.01 Initial RMS Z values bonds: 0.124433 angles: 0.358074 torsions: N/A planes: 0.729691 non-bonded: 3.52861 chiral vol: 0.333949 rama plot: -152.856 start_pos: N/A Minimum found (iteration number 331) at -774.494 Final Estimated RMS Z Scores: bonds: 1.84442 angles: 1.23453 torsions: N/A planes: 0.802009 non-bonded: 0.16287 chiral vol: 0.395276 rama plot: -152.405 start_pos: N/A SUCCESS TIME:: (dragged refinement): 243.894 Refinement elapsed time: 0.043 INFO:: replace_coords: 19 atoms updated. centering on B 27 CA created 21 bond restraints created 23 angle restraints created 1 plane restraints created 2 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 26 and 28 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -916.666 Initial RMS Z values bonds: 1.69038 angles: 1.14794 torsions: N/A planes: 0.731019 non-bonded: 0.101794 chiral vol: 0.434914 rama plot: -157.023 start_pos: N/A Minimum found (iteration number 377) at -921.843 Final Estimated RMS Z Scores: bonds: 1.69313 angles: 1.13626 torsions: N/A planes: 0.545361 non-bonded: 0.101535 chiral vol: 0.314059 rama plot: -157.047 start_pos: N/A SUCCESS TIME:: (dragged refinement): 244.526 Refinement elapsed time: 0.058 INFO:: replace_coords: 22 atoms updated. centering on B 28 CA created 25 bond restraints created 29 angle restraints created 1 plane restraints created 3 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 27 and 29 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -479.283 Initial RMS Z values bonds: 1.57136 angles: 1.03848 torsions: N/A planes: 0.658742 non-bonded: 1.6806 chiral vol: 0.307542 rama plot: -189.398 start_pos: N/A Minimum found (iteration number 66) at -1144.95 Final Estimated RMS Z Scores: bonds: 1.44283 angles: 1.0331 torsions: N/A planes: 0.76317 non-bonded: 0.081458 chiral vol: 0.436978 rama plot: -191.058 start_pos: N/A SUCCESS TIME:: (dragged refinement): 245.206 Refinement elapsed time: 0.078 INFO:: replace_coords: 25 atoms updated. centering on B 29 CA created 30 bond restraints created 36 angle restraints created 2 plane restraints created 3 chiral vol restraints created 71 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 28 and 30 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1343.2 Initial RMS Z values bonds: 1.33253 angles: 0.933356 torsions: N/A planes: 0.651946 non-bonded: 0.0623093 chiral vol: 0.439026 rama plot: -187.224 start_pos: N/A Minimum found (iteration number 281) at -1346.55 Final Estimated RMS Z Scores: bonds: 1.33665 angles: 0.938874 torsions: N/A planes: 0.641512 non-bonded: 0.0624552 chiral vol: 0.451719 rama plot: -188.609 start_pos: N/A SUCCESS TIME:: (dragged refinement): 245.939 Refinement elapsed time: 0.058 INFO:: replace_coords: 30 atoms updated. centering on B 30 CA created 24 bond restraints created 28 angle restraints created 1 plane restraints created 3 chiral vol restraints created 56 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 29 and 31 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1321.97 Initial RMS Z values bonds: 1.47379 angles: 1.0336 torsions: N/A planes: 0.585687 non-bonded: 0 chiral vol: 0.361162 rama plot: -201.321 start_pos: N/A Minimum found (iteration number 307) at -1434.64 Final Estimated RMS Z Scores: bonds: 0.137614 angles: 0.275724 torsions: N/A planes: 0.52585 non-bonded: 0 chiral vol: 0.221658 rama plot: -204.039 start_pos: N/A SUCCESS TIME:: (dragged refinement): 246.67 Refinement elapsed time: 0.051 INFO:: replace_coords: 25 atoms updated. centering on B 31 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 30 and 32 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1416.75 Initial RMS Z values bonds: 0.125596 angles: 0.318911 torsions: N/A planes: 0.462703 non-bonded: 0 chiral vol: 0.449298 rama plot: -192.451 start_pos: N/A Minimum found (iteration number 369) at -1420.35 Final Estimated RMS Z Scores: bonds: 0.144046 angles: 0.333524 torsions: N/A planes: 0.622159 non-bonded: 0 chiral vol: 0.487616 rama plot: -197.237 start_pos: N/A SUCCESS TIME:: (dragged refinement): 247.329 Refinement elapsed time: 0.068 INFO:: replace_coords: 27 atoms updated. centering on B 32 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 3 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 31 and 33 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1368.96 Initial RMS Z values bonds: 0.157197 angles: 0.355793 torsions: N/A planes: 0.462403 non-bonded: 0 chiral vol: 0.480545 rama plot: -198.117 start_pos: N/A Minimum found (iteration number 247) at -1373.77 Final Estimated RMS Z Scores: bonds: 0.158257 angles: 0.400515 torsions: N/A planes: 0.355152 non-bonded: 0 chiral vol: 0.508719 rama plot: -197.752 start_pos: N/A SUCCESS TIME:: (dragged refinement): 247.977 Refinement elapsed time: 0.043 INFO:: replace_coords: 23 atoms updated. centering on B 33 CA created 18 bond restraints created 19 angle restraints created 2 plane restraints created 2 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 32 and 34 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1236.05 Initial RMS Z values bonds: 0.153225 angles: 0.454253 torsions: N/A planes: 0.448617 non-bonded: 0 chiral vol: 0.616377 rama plot: -177.183 start_pos: N/A Minimum found (iteration number 319) at -1238.47 Final Estimated RMS Z Scores: bonds: 0.122564 angles: 0.429949 torsions: N/A planes: 0.371113 non-bonded: 0 chiral vol: 0.559951 rama plot: -176.642 start_pos: N/A SUCCESS TIME:: (dragged refinement): 248.645 Refinement elapsed time: 0.046 INFO:: replace_coords: 21 atoms updated. centering on B 34 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 33 and 35 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1187.97 Initial RMS Z values bonds: 0.128531 angles: 0.383399 torsions: N/A planes: 0.40376 non-bonded: 0 chiral vol: 0.181928 rama plot: -173.783 start_pos: N/A Minimum found (iteration number 174) at -1189.08 Final Estimated RMS Z Scores: bonds: 0.12825 angles: 0.367866 torsions: N/A planes: 0.390371 non-bonded: 0 chiral vol: 0.162858 rama plot: -173.971 start_pos: N/A SUCCESS TIME:: (dragged refinement): 249.276 Refinement elapsed time: 0.026 INFO:: replace_coords: 19 atoms updated. centering on B 35 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 34 and 36 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1052.37 Initial RMS Z values bonds: 0.12358 angles: 0.3481 torsions: N/A planes: 0.528229 non-bonded: 0 chiral vol: 0.142108 rama plot: -174.279 start_pos: N/A Minimum found (iteration number 230) at -1052.82 Final Estimated RMS Z Scores: bonds: 0.108249 angles: 0.32985 torsions: N/A planes: 0.526612 non-bonded: 0 chiral vol: 0.129702 rama plot: -174.333 start_pos: N/A SUCCESS TIME:: (dragged refinement): 249.876 Refinement elapsed time: 0.03 INFO:: replace_coords: 18 atoms updated. centering on B 36 CA created 23 bond restraints created 27 angle restraints created 1 plane restraints created 3 chiral vol restraints created 54 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 35 and 37 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1222.91 Initial RMS Z values bonds: 0.113646 angles: 0.3217 torsions: N/A planes: 0.603294 non-bonded: 0 chiral vol: 0.241504 rama plot: -180.972 start_pos: N/A Minimum found (iteration number 244) at -1224.1 Final Estimated RMS Z Scores: bonds: 0.122862 angles: 0.312568 torsions: N/A planes: 0.562124 non-bonded: 0 chiral vol: 0.246332 rama plot: -181.493 start_pos: N/A SUCCESS TIME:: (dragged refinement): 250.43 Refinement elapsed time: 0.041 INFO:: replace_coords: 25 atoms updated. centering on B 37 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 36 and 38 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1197.82 Initial RMS Z values bonds: 0.113439 angles: 0.411815 torsions: N/A planes: 0.739495 non-bonded: 0 chiral vol: 0.685096 rama plot: -191.827 start_pos: N/A Minimum found (iteration number 7) at -1201.98 Final Estimated RMS Z Scores: bonds: 0.121459 angles: 0.393346 torsions: N/A planes: 0.81516 non-bonded: 0 chiral vol: 0.677325 rama plot: -193.569 start_pos: N/A SUCCESS TIME:: (dragged refinement): 251.063 Refinement elapsed time: 0.074 INFO:: replace_coords: 27 atoms updated. centering on B 38 CA created 26 bond restraints created 30 angle restraints created 3 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 37 and 39 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1182.71 Initial RMS Z values bonds: 0.108107 angles: 0.425137 torsions: N/A planes: 0.936227 non-bonded: 0 chiral vol: 0.695123 rama plot: -181.36 start_pos: N/A Minimum found (iteration number 112) at -1192.28 Final Estimated RMS Z Scores: bonds: 0.11566 angles: 0.466027 torsions: N/A planes: 0.823 non-bonded: 0 chiral vol: 0.80041 rama plot: -184.256 start_pos: N/A SUCCESS TIME:: (dragged refinement): 251.673 Refinement elapsed time: 0.096 INFO:: replace_coords: 28 atoms updated. centering on B 39 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 38 and 40 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1063.29 Initial RMS Z values bonds: 0.115168 angles: 0.482783 torsions: N/A planes: 0.787725 non-bonded: 3.46244e-08 chiral vol: 0.784819 rama plot: -194.15 start_pos: N/A Minimum found (iteration number 2) at -1073.06 Final Estimated RMS Z Scores: bonds: 0.118286 angles: 0.468453 torsions: N/A planes: 0.788979 non-bonded: 1.20094e-06 chiral vol: 0.730869 rama plot: -197.252 start_pos: N/A SUCCESS TIME:: (dragged refinement): 252.352 Refinement elapsed time: 0.144 INFO:: replace_coords: 28 atoms updated. centering on B 40 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 39 and 41 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1008.1 Initial RMS Z values bonds: 0.117298 angles: 0.360361 torsions: N/A planes: 0.733185 non-bonded: 1.04653e-06 chiral vol: 0.298452 rama plot: -183.795 start_pos: N/A Minimum found (iteration number 299) at -1010.78 Final Estimated RMS Z Scores: bonds: 0.0973026 angles: 0.342463 torsions: N/A planes: 0.7805 non-bonded: 3.0009e-07 chiral vol: 0.306108 rama plot: -184.956 start_pos: N/A SUCCESS TIME:: (dragged refinement): 253.014 Refinement elapsed time: 0.128 INFO:: replace_coords: 28 atoms updated. centering on B 41 CA created 23 bond restraints created 25 angle restraints created 2 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 40 and 42 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -916.546 Initial RMS Z values bonds: 0.0930212 angles: 0.351178 torsions: N/A planes: 0.805089 non-bonded: 3.66922e-07 chiral vol: 0.357738 rama plot: -185.235 start_pos: N/A Minimum found (iteration number 333) at -919.957 Final Estimated RMS Z Scores: bonds: 0.0847975 angles: 0.334853 torsions: N/A planes: 0.831958 non-bonded: 1.1822e-08 chiral vol: 0.320911 rama plot: -185.585 start_pos: N/A SUCCESS TIME:: (dragged refinement): 253.624 Refinement elapsed time: 0.123 INFO:: replace_coords: 26 atoms updated. centering on B 42 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 41 and 43 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -966.789 Initial RMS Z values bonds: 0.0973419 angles: 0.314516 torsions: N/A planes: 0.886779 non-bonded: 1.07552e-09 chiral vol: 0.324987 rama plot: -182.227 start_pos: N/A Minimum found (iteration number 364) at -975.602 Final Estimated RMS Z Scores: bonds: 0.0919569 angles: 0.341953 torsions: N/A planes: 0.829381 non-bonded: 4.60065e-08 chiral vol: 0.323959 rama plot: -185.51 start_pos: N/A SUCCESS TIME:: (dragged refinement): 254.201 Refinement elapsed time: 0.054 INFO:: replace_coords: 22 atoms updated. centering on B 43 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 42 and 44 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1057.68 Initial RMS Z values bonds: 0.111966 angles: 0.40136 torsions: N/A planes: 0.896502 non-bonded: 0 chiral vol: 0.274242 rama plot: -182.468 start_pos: N/A Minimum found (iteration number 292) at -1060.32 Final Estimated RMS Z Scores: bonds: 0.0905252 angles: 0.356995 torsions: N/A planes: 0.861718 non-bonded: 0 chiral vol: 0.239625 rama plot: -182.857 start_pos: N/A SUCCESS TIME:: (dragged refinement): 254.76 Refinement elapsed time: 0.04 INFO:: replace_coords: 21 atoms updated. centering on B 44 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 3 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 43 and 45 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -506.113 Initial RMS Z values bonds: 0.0965252 angles: 0.307665 torsions: N/A planes: 0.865481 non-bonded: 1.98242 chiral vol: 0.0672361 rama plot: -191.157 start_pos: N/A Minimum found (iteration number 359) at -1019.88 Final Estimated RMS Z Scores: bonds: 1.58154 angles: 1.11384 torsions: N/A planes: 0.820675 non-bonded: 0.0983617 chiral vol: 0.181445 rama plot: -191.969 start_pos: N/A SUCCESS TIME:: (dragged refinement): 255.372 Refinement elapsed time: 0.052 INFO:: replace_coords: 22 atoms updated. centering on B 45 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 44 and 46 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1037.21 Initial RMS Z values bonds: 1.58331 angles: 1.11068 torsions: N/A planes: 0.620428 non-bonded: 0.104112 chiral vol: 0.153743 rama plot: -178.94 start_pos: N/A Minimum found (iteration number 307) at -1038.8 Final Estimated RMS Z Scores: bonds: 1.58075 angles: 1.11304 torsions: N/A planes: 0.668414 non-bonded: 0.103857 chiral vol: 0.140287 rama plot: -179.812 start_pos: N/A SUCCESS TIME:: (dragged refinement): 255.987 Refinement elapsed time: 0.043 INFO:: replace_coords: 22 atoms updated. centering on B 46 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 45 and 47 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1152.62 Initial RMS Z values bonds: 1.55046 angles: 1.09546 torsions: N/A planes: 0.436405 non-bonded: 2.14341e-05 chiral vol: 0.100044 rama plot: -176.699 start_pos: N/A Minimum found (iteration number 340) at -1256.21 Final Estimated RMS Z Scores: bonds: 0.142111 angles: 0.348236 torsions: N/A planes: 0.43987 non-bonded: 1.10911e-05 chiral vol: 0.100079 rama plot: -177.887 start_pos: N/A SUCCESS TIME:: (dragged refinement): 256.617 Refinement elapsed time: 0.051 INFO:: replace_coords: 23 atoms updated. centering on B 47 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 46 and 48 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1250.16 Initial RMS Z values bonds: 0.175917 angles: 0.274167 torsions: N/A planes: 0.379112 non-bonded: 1.27922e-05 chiral vol: 0.172683 rama plot: -174.391 start_pos: N/A Minimum found (iteration number 257) at -1256.13 Final Estimated RMS Z Scores: bonds: 0.148107 angles: 0.233947 torsions: N/A planes: 0.41726 non-bonded: 1.58019e-05 chiral vol: 0.137571 rama plot: -176.719 start_pos: N/A SUCCESS TIME:: (dragged refinement): 257.227 Refinement elapsed time: 0.038 INFO:: replace_coords: 22 atoms updated. centering on B 48 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 47 and 49 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1280.44 Initial RMS Z values bonds: 0.14396 angles: 0.28377 torsions: N/A planes: 0.417109 non-bonded: 8.6033e-06 chiral vol: 0.250403 rama plot: -175.815 start_pos: N/A Minimum found (iteration number 390) at -1282.92 Final Estimated RMS Z Scores: bonds: 0.147259 angles: 0.319968 torsions: N/A planes: 0.412319 non-bonded: 1.07937e-05 chiral vol: 0.27747 rama plot: -175.963 start_pos: N/A SUCCESS TIME:: (dragged refinement): 257.86 Refinement elapsed time: 0.068 INFO:: replace_coords: 27 atoms updated. centering on B 49 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 2 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 48 and 50 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1101.82 Initial RMS Z values bonds: 0.155896 angles: 0.336371 torsions: N/A planes: 0.630142 non-bonded: 0 chiral vol: 0.318868 rama plot: -171.148 start_pos: N/A Minimum found (iteration number 262) at -1104.67 Final Estimated RMS Z Scores: bonds: 0.193922 angles: 0.34886 torsions: N/A planes: 0.633136 non-bonded: 0 chiral vol: 0.374355 rama plot: -171.984 start_pos: N/A SUCCESS TIME:: (dragged refinement): 258.387 Refinement elapsed time: 0.041 INFO:: replace_coords: 22 atoms updated. centering on B 50 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 49 and 51 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1340.87 Initial RMS Z values bonds: 0.143101 angles: 0.313556 torsions: N/A planes: 0.744833 non-bonded: 0 chiral vol: 0.319908 rama plot: -184.034 start_pos: N/A Minimum found (iteration number 378) at -1344.73 Final Estimated RMS Z Scores: bonds: 0.137008 angles: 0.303294 torsions: N/A planes: 0.722081 non-bonded: 0 chiral vol: 0.259722 rama plot: -185.62 start_pos: N/A SUCCESS TIME:: (dragged refinement): 258.924 Refinement elapsed time: 0.067 INFO:: replace_coords: 28 atoms updated. centering on B 51 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 50 and 52 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1454.42 Initial RMS Z values bonds: 0.0923156 angles: 0.305041 torsions: N/A planes: 0.818792 non-bonded: 0 chiral vol: 0.152669 rama plot: -183.123 start_pos: N/A Minimum found (iteration number 202) at -1455.05 Final Estimated RMS Z Scores: bonds: 0.0905964 angles: 0.311382 torsions: N/A planes: 0.80662 non-bonded: 0 chiral vol: 0.162498 rama plot: -183.232 start_pos: N/A SUCCESS TIME:: (dragged refinement): 259.473 Refinement elapsed time: 0.041 INFO:: replace_coords: 28 atoms updated. centering on B 52 CA created 34 bond restraints created 42 angle restraints created 3 plane restraints created 3 chiral vol restraints created 82 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 51 and 53 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1649.79 Initial RMS Z values bonds: 0.0965773 angles: 0.260376 torsions: N/A planes: 0.789828 non-bonded: 0 chiral vol: 0.175319 rama plot: -191.713 start_pos: N/A Minimum found (iteration number 250) at -1650.36 Final Estimated RMS Z Scores: bonds: 0.0910533 angles: 0.247798 torsions: N/A planes: 0.810114 non-bonded: 0 chiral vol: 0.155946 rama plot: -191.818 start_pos: N/A SUCCESS TIME:: (dragged refinement): 260.073 Refinement elapsed time: 0.06 INFO:: replace_coords: 34 atoms updated. centering on B 53 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 52 and 54 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1469.08 Initial RMS Z values bonds: 0.120105 angles: 0.287211 torsions: N/A planes: 0.695782 non-bonded: 0 chiral vol: 0.299672 rama plot: -177.917 start_pos: N/A Minimum found (iteration number 394) at -1469.87 Final Estimated RMS Z Scores: bonds: 0.127568 angles: 0.288926 torsions: N/A planes: 0.716223 non-bonded: 0 chiral vol: 0.292024 rama plot: -177.994 start_pos: N/A SUCCESS TIME:: (dragged refinement): 260.741 Refinement elapsed time: 0.079 INFO:: replace_coords: 31 atoms updated. centering on B 54 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 53 and 55 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1498.57 Initial RMS Z values bonds: 0.175254 angles: 0.254181 torsions: N/A planes: 0.555456 non-bonded: 0 chiral vol: 0.263874 rama plot: -177.854 start_pos: N/A Minimum found (iteration number 191) at -1500.35 Final Estimated RMS Z Scores: bonds: 0.167083 angles: 0.254614 torsions: N/A planes: 0.51729 non-bonded: 0 chiral vol: 0.279159 rama plot: -178.503 start_pos: N/A SUCCESS TIME:: (dragged refinement): 261.511 Refinement elapsed time: 0.12 INFO:: replace_coords: 31 atoms updated. centering on B 55 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 54 and 56 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1497.01 Initial RMS Z values bonds: 0.197736 angles: 0.269031 torsions: N/A planes: 1.11913 non-bonded: 0 chiral vol: 0.247701 rama plot: -179.649 start_pos: N/A Minimum found (iteration number 241) at -1497.86 Final Estimated RMS Z Scores: bonds: 0.190002 angles: 0.28016 torsions: N/A planes: 1.1108 non-bonded: 0 chiral vol: 0.259009 rama plot: -180.345 start_pos: N/A SUCCESS TIME:: (dragged refinement): 262.21 Refinement elapsed time: 0.046 INFO:: replace_coords: 28 atoms updated. centering on B 56 CA created 24 bond restraints created 29 angle restraints created 1 plane restraints created 4 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 55 and 57 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1467 Initial RMS Z values bonds: 0.218586 angles: 0.497865 torsions: N/A planes: 1.26441 non-bonded: 0 chiral vol: 0.394932 rama plot: -177.733 start_pos: N/A Minimum found (iteration number 217) at -1468.22 Final Estimated RMS Z Scores: bonds: 0.240359 angles: 0.506719 torsions: N/A planes: 1.24098 non-bonded: 0 chiral vol: 0.404253 rama plot: -178.345 start_pos: N/A SUCCESS TIME:: (dragged refinement): 262.907 Refinement elapsed time: 0.036 INFO:: replace_coords: 26 atoms updated. centering on B 57 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 56 and 58 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1324.93 Initial RMS Z values bonds: 0.230401 angles: 0.528328 torsions: N/A planes: 1.37707 non-bonded: 7.4272e-05 chiral vol: 0.361511 rama plot: -180.252 start_pos: N/A unexpected error from gsl_multimin_fdfminimizer_iterate Error in gsl_multimin_fdfminimizer_iterate was GSL_ENOPROG Final Estimated RMS Z Scores bonds: 0.229123 angles: 0.527252 torsions: N/A planes: 1.39759 non-bonded: 4.85871e-05 chiral vol: 0.362457 rama plot: -180.437 start_pos: N/A NOPROGRESS TIME:: (dragged refinement): 263.622 Refinement elapsed time: 0.03 INFO:: replace_coords: 22 atoms updated. centering on B 58 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 57 and 59 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1273.27 Initial RMS Z values bonds: 0.21177 angles: 0.622445 torsions: N/A planes: 1.39879 non-bonded: 5.18862e-05 chiral vol: 0.431537 rama plot: -176.869 start_pos: N/A Minimum found (iteration number 219) at -1275.47 Final Estimated RMS Z Scores: bonds: 0.22567 angles: 0.596988 torsions: N/A planes: 1.41419 non-bonded: 4.61991e-05 chiral vol: 0.480206 rama plot: -177.692 start_pos: N/A SUCCESS TIME:: (dragged refinement): 264.338 Refinement elapsed time: 0.034 INFO:: replace_coords: 22 atoms updated. centering on B 59 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 5 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 58 and 60 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -670.411 Initial RMS Z values bonds: 0.184121 angles: 0.457781 torsions: N/A planes: 0.804818 non-bonded: 1.80833 chiral vol: 0.344457 rama plot: -180.252 start_pos: N/A Minimum found (iteration number 344) at -1142.53 Final Estimated RMS Z Scores: bonds: 1.5544 angles: 1.16455 torsions: N/A planes: 0.773371 non-bonded: 0.0946817 chiral vol: 0.248742 rama plot: -180.761 start_pos: N/A SUCCESS TIME:: (dragged refinement): 265.044 Refinement elapsed time: 0.048 INFO:: replace_coords: 22 atoms updated. centering on B 60 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 59 and 61 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -980.357 Initial RMS Z values bonds: 1.70064 angles: 1.27518 torsions: N/A planes: 0.754412 non-bonded: 0.144084 chiral vol: 0.320119 rama plot: -167.624 start_pos: N/A Minimum found (iteration number 193) at -983.65 Final Estimated RMS Z Scores: bonds: 1.70195 angles: 1.26609 torsions: N/A planes: 0.754205 non-bonded: 0.144135 chiral vol: 0.314128 rama plot: -168.977 start_pos: N/A SUCCESS TIME:: (dragged refinement): 265.716 Refinement elapsed time: 0.027 INFO:: replace_coords: 18 atoms updated. centering on B 61 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 60 and 62 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -898.495 Initial RMS Z values bonds: 1.79377 angles: 1.3248 torsions: N/A planes: 0.677579 non-bonded: 0 chiral vol: 0.0829854 rama plot: -170.763 start_pos: N/A Minimum found (iteration number 305) at -1000.45 Final Estimated RMS Z Scores: bonds: 0.117072 angles: 0.482299 torsions: N/A planes: 0.575471 non-bonded: 0 chiral vol: 0.103948 rama plot: -170.76 start_pos: N/A SUCCESS TIME:: (dragged refinement): 266.397 Refinement elapsed time: 0.034 INFO:: replace_coords: 16 atoms updated. centering on B 62 CA created 17 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 61 and 63 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1126.51 Initial RMS Z values bonds: 0.111841 angles: 0.419886 torsions: N/A planes: 0.569139 non-bonded: 0 chiral vol: 0.187498 rama plot: -168.763 start_pos: N/A Minimum found (iteration number 241) at -1127.97 Final Estimated RMS Z Scores: bonds: 0.111502 angles: 0.384281 torsions: N/A planes: 0.646363 non-bonded: 0 chiral vol: 0.223577 rama plot: -169.299 start_pos: N/A SUCCESS TIME:: (dragged refinement): 267.067 Refinement elapsed time: 0.032 INFO:: replace_coords: 20 atoms updated. centering on B 63 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 62 and 64 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1230.59 Initial RMS Z values bonds: 0.11391 angles: 0.332277 torsions: N/A planes: 0.656062 non-bonded: 0 chiral vol: 0.186479 rama plot: -164.53 start_pos: N/A Minimum found (iteration number 286) at -1238.46 Final Estimated RMS Z Scores: bonds: 0.134727 angles: 0.362511 torsions: N/A planes: 0.750331 non-bonded: 2.06474e-05 chiral vol: 0.166982 rama plot: -171.346 start_pos: N/A SUCCESS TIME:: (dragged refinement): 267.811 Refinement elapsed time: 0.044 INFO:: replace_coords: 23 atoms updated. centering on B 64 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 63 and 65 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1412.06 Initial RMS Z values bonds: 0.12876 angles: 0.369624 torsions: N/A planes: 0.597721 non-bonded: 1.78319e-05 chiral vol: 0.166043 rama plot: -170.143 start_pos: N/A Minimum found (iteration number 326) at -1425.48 Final Estimated RMS Z Scores: bonds: 0.134126 angles: 0.330671 torsions: N/A planes: 0.606967 non-bonded: 0 chiral vol: 0.17611 rama plot: -170.585 start_pos: N/A SUCCESS TIME:: (dragged refinement): 268.609 Refinement elapsed time: 0.062 INFO:: replace_coords: 29 atoms updated. centering on B 65 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 64 and 66 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1179.54 Initial RMS Z values bonds: 0.141052 angles: 0.346683 torsions: N/A planes: 0.802133 non-bonded: 0 chiral vol: 0.12691 rama plot: -152.066 start_pos: N/A Minimum found (iteration number 217) at -1183.03 Final Estimated RMS Z Scores: bonds: 0.128093 angles: 0.328965 torsions: N/A planes: 0.898949 non-bonded: 0 chiral vol: 0.12445 rama plot: -152.837 start_pos: N/A SUCCESS TIME:: (dragged refinement): 269.354 Refinement elapsed time: 0.035 INFO:: replace_coords: 22 atoms updated. centering on B 66 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 65 and 67 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1185.83 Initial RMS Z values bonds: 0.135233 angles: 0.385876 torsions: N/A planes: 0.978515 non-bonded: 0 chiral vol: 0.315434 rama plot: -160.816 start_pos: N/A Minimum found (iteration number 278) at -1190.36 Final Estimated RMS Z Scores: bonds: 0.161888 angles: 0.456711 torsions: N/A planes: 0.900267 non-bonded: 0 chiral vol: 0.360489 rama plot: -164.588 start_pos: N/A SUCCESS TIME:: (dragged refinement): 270.055 Refinement elapsed time: 0.041 INFO:: replace_coords: 22 atoms updated. centering on B 67 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 66 and 68 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1252.85 Initial RMS Z values bonds: 0.171541 angles: 0.443078 torsions: N/A planes: 0.906006 non-bonded: 0 chiral vol: 0.404888 rama plot: -156.388 start_pos: N/A Minimum found (iteration number 248) at -1256.72 Final Estimated RMS Z Scores: bonds: 0.14074 angles: 0.420497 torsions: N/A planes: 0.793878 non-bonded: 0 chiral vol: 0.380584 rama plot: -156.238 start_pos: N/A SUCCESS TIME:: (dragged refinement): 270.74 Refinement elapsed time: 0.039 INFO:: replace_coords: 22 atoms updated. centering on B 68 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 67 and 69 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1547.31 Initial RMS Z values bonds: 0.197166 angles: 0.385683 torsions: N/A planes: 1.20057 non-bonded: 0 chiral vol: 0.329744 rama plot: -173.531 start_pos: N/A Minimum found (iteration number 181) at -1547.69 Final Estimated RMS Z Scores: bonds: 0.179143 angles: 0.387279 torsions: N/A planes: 1.19014 non-bonded: 0 chiral vol: 0.329961 rama plot: -173.627 start_pos: N/A SUCCESS TIME:: (dragged refinement): 271.469 Refinement elapsed time: 0.038 INFO:: replace_coords: 29 atoms updated. centering on B 69 CA created 27 bond restraints created 30 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 68 and 70 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1595.48 Initial RMS Z values bonds: 0.208387 angles: 0.371224 torsions: N/A planes: 1.1128 non-bonded: 2.8375e-05 chiral vol: 0.187541 rama plot: -178.898 start_pos: N/A Minimum found (iteration number 169) at -1595.71 Final Estimated RMS Z Scores: bonds: 0.190254 angles: 0.360919 torsions: N/A planes: 1.11669 non-bonded: 3.29766e-05 chiral vol: 0.190726 rama plot: -178.831 start_pos: N/A SUCCESS TIME:: (dragged refinement): 272.191 Refinement elapsed time: 0.035 INFO:: replace_coords: 30 atoms updated. centering on B 70 CA created 24 bond restraints created 27 angle restraints created 1 plane restraints created 5 chiral vol restraints created 57 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 69 and 71 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1438.85 Initial RMS Z values bonds: 0.226599 angles: 0.393624 torsions: N/A planes: 1.17669 non-bonded: 4.75413e-05 chiral vol: 0.158663 rama plot: -179.726 start_pos: N/A Minimum found (iteration number 223) at -1439.4 Final Estimated RMS Z Scores: bonds: 0.233241 angles: 0.398198 torsions: N/A planes: 1.15681 non-bonded: 4.14257e-05 chiral vol: 0.15977 rama plot: -179.759 start_pos: N/A SUCCESS TIME:: (dragged refinement): 272.931 Refinement elapsed time: 0.041 INFO:: replace_coords: 27 atoms updated. centering on B 71 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 5 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 70 and 72 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1202.76 Initial RMS Z values bonds: 0.26569 angles: 0.438224 torsions: N/A planes: 1.35483 non-bonded: 6.01793e-05 chiral vol: 0.175177 rama plot: -180.295 start_pos: N/A Minimum found (iteration number 285) at -1205.42 Final Estimated RMS Z Scores: bonds: 0.248138 angles: 0.443164 torsions: N/A planes: 1.2796 non-bonded: 6.16681e-05 chiral vol: 0.177758 rama plot: -180.428 start_pos: N/A SUCCESS TIME:: (dragged refinement): 273.601 Refinement elapsed time: 0.04 INFO:: replace_coords: 21 atoms updated. centering on B 72 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 71 and 73 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1071.13 Initial RMS Z values bonds: 0.225089 angles: 0.429296 torsions: N/A planes: 0.717098 non-bonded: 4.4724e-05 chiral vol: 0.204 rama plot: -173.349 start_pos: N/A Minimum found (iteration number 21) at -1072.65 Final Estimated RMS Z Scores: bonds: 0.226762 angles: 0.478787 torsions: N/A planes: 0.673028 non-bonded: 5.37945e-05 chiral vol: 0.177841 rama plot: -174.206 start_pos: N/A SUCCESS TIME:: (dragged refinement): 274.215 Refinement elapsed time: 0.047 INFO:: replace_coords: 17 atoms updated. centering on B 73 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 72 and 74 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1057.28 Initial RMS Z values bonds: 0.158873 angles: 0.442127 torsions: N/A planes: 0.650801 non-bonded: 0 chiral vol: 0.388391 rama plot: -185.717 start_pos: N/A Minimum found (iteration number 280) at -1060.91 Final Estimated RMS Z Scores: bonds: 0.19457 angles: 0.476718 torsions: N/A planes: 0.62172 non-bonded: 0 chiral vol: 0.364238 rama plot: -186.829 start_pos: N/A SUCCESS TIME:: (dragged refinement): 274.756 Refinement elapsed time: 0.036 INFO:: replace_coords: 18 atoms updated. centering on B 74 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 73 and 75 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1011.48 Initial RMS Z values bonds: 0.164161 angles: 0.460351 torsions: N/A planes: 0.600376 non-bonded: 0 chiral vol: 0.350594 rama plot: -188.696 start_pos: N/A Minimum found (iteration number 293) at -1015.21 Final Estimated RMS Z Scores: bonds: 0.159419 angles: 0.443089 torsions: N/A planes: 0.623315 non-bonded: 0 chiral vol: 0.413164 rama plot: -190.28 start_pos: N/A SUCCESS TIME:: (dragged refinement): 275.272 Refinement elapsed time: 0.038 INFO:: replace_coords: 18 atoms updated. centering on B 75 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 74 and 76 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1024.45 Initial RMS Z values bonds: 0.152578 angles: 0.233593 torsions: N/A planes: 0.572127 non-bonded: 0 chiral vol: 0.312777 rama plot: -193.28 start_pos: N/A Minimum found (iteration number 297) at -1029.28 Final Estimated RMS Z Scores: bonds: 0.147382 angles: 0.231914 torsions: N/A planes: 0.470992 non-bonded: 0 chiral vol: 0.294576 rama plot: -195.122 start_pos: N/A SUCCESS TIME:: (dragged refinement): 275.743 Refinement elapsed time: 0.041 INFO:: replace_coords: 21 atoms updated. centering on B 76 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 75 and 77 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -912.384 Initial RMS Z values bonds: 0.169331 angles: 0.257626 torsions: N/A planes: 0.413525 non-bonded: 0 chiral vol: 0.118091 rama plot: -171.908 start_pos: N/A Minimum found (iteration number 292) at -916.698 Final Estimated RMS Z Scores: bonds: 0.147936 angles: 0.261563 torsions: N/A planes: 0.411579 non-bonded: 7.14591e-06 chiral vol: 0.127782 rama plot: -172.715 start_pos: N/A SUCCESS TIME:: (dragged refinement): 276.192 Refinement elapsed time: 0.044 INFO:: replace_coords: 21 atoms updated. centering on B 77 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 76 and 78 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1075.12 Initial RMS Z values bonds: 0.182154 angles: 0.358592 torsions: N/A planes: 0.38326 non-bonded: 5.40478e-06 chiral vol: 0.15499 rama plot: -158.317 start_pos: N/A Minimum found (iteration number 341) at -1076.68 Final Estimated RMS Z Scores: bonds: 0.202142 angles: 0.376451 torsions: N/A planes: 0.325802 non-bonded: 5.22221e-06 chiral vol: 0.16752 rama plot: -158.768 start_pos: N/A SUCCESS TIME:: (dragged refinement): 276.714 Refinement elapsed time: 0.056 INFO:: replace_coords: 25 atoms updated. centering on B 78 CA created 23 bond restraints created 26 angle restraints created 3 plane restraints created 3 chiral vol restraints created 55 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 77 and 79 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1232.67 Initial RMS Z values bonds: 0.228496 angles: 0.394747 torsions: N/A planes: 0.333836 non-bonded: 0 chiral vol: 0.17941 rama plot: -158.815 start_pos: N/A Minimum found (iteration number 268) at -1234.66 Final Estimated RMS Z Scores: bonds: 0.22163 angles: 0.366067 torsions: N/A planes: 0.45 non-bonded: 0 chiral vol: 0.161831 rama plot: -159.492 start_pos: N/A SUCCESS TIME:: (dragged refinement): 277.267 Refinement elapsed time: 0.049 INFO:: replace_coords: 26 atoms updated. centering on B 79 CA created 27 bond restraints created 32 angle restraints created 3 plane restraints created 3 chiral vol restraints created 65 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 78 and 80 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1494.68 Initial RMS Z values bonds: 0.21341 angles: 0.351298 torsions: N/A planes: 0.326971 non-bonded: 0 chiral vol: 0.173694 rama plot: -166.664 start_pos: N/A Minimum found (iteration number 197) at -1495.66 Final Estimated RMS Z Scores: bonds: 0.204476 angles: 0.354291 torsions: N/A planes: 0.331817 non-bonded: 0 chiral vol: 0.171129 rama plot: -167.166 start_pos: N/A SUCCESS TIME:: (dragged refinement): 277.898 Refinement elapsed time: 0.042 INFO:: replace_coords: 29 atoms updated. centering on B 80 CA created 31 bond restraints created 38 angle restraints created 3 plane restraints created 3 chiral vol restraints created 75 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 79 and 81 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1619.65 Initial RMS Z values bonds: 0.20329 angles: 0.257509 torsions: N/A planes: 0.715777 non-bonded: 0 chiral vol: 0.158355 rama plot: -181.036 start_pos: N/A Minimum found (iteration number 190) at -1620.03 Final Estimated RMS Z Scores: bonds: 0.204897 angles: 0.249861 torsions: N/A planes: 0.756667 non-bonded: 0 chiral vol: 0.153727 rama plot: -180.908 start_pos: N/A SUCCESS TIME:: (dragged refinement): 278.605 Refinement elapsed time: 0.042 INFO:: replace_coords: 32 atoms updated. centering on B 81 CA created 30 bond restraints created 37 angle restraints created 2 plane restraints created 4 chiral vol restraints created 73 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 80 and 82 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1610.7 Initial RMS Z values bonds: 0.18474 angles: 0.195672 torsions: N/A planes: 0.877375 non-bonded: 0 chiral vol: 0.138552 rama plot: -180.087 start_pos: N/A Minimum found (iteration number 169) at -1612.67 Final Estimated RMS Z Scores: bonds: 0.190171 angles: 0.205125 torsions: N/A planes: 0.845276 non-bonded: 0 chiral vol: 0.116563 rama plot: -180.743 start_pos: N/A SUCCESS TIME:: (dragged refinement): 279.356 Refinement elapsed time: 0.036 INFO:: replace_coords: 31 atoms updated. centering on B 82 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 81 and 83 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1355.96 Initial RMS Z values bonds: 0.183483 angles: 0.207334 torsions: N/A planes: 0.972316 non-bonded: 0 chiral vol: 0.0786332 rama plot: -177.434 start_pos: N/A Minimum found (iteration number 210) at -1359.01 Final Estimated RMS Z Scores: bonds: 0.169107 angles: 0.182808 torsions: N/A planes: 0.891241 non-bonded: 0 chiral vol: 0.0951137 rama plot: -178.094 start_pos: N/A SUCCESS TIME:: (dragged refinement): 280.093 Refinement elapsed time: 0.036 INFO:: replace_coords: 23 atoms updated. centering on B 83 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 82 and 84 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1176.09 Initial RMS Z values bonds: 0.14985 angles: 0.337245 torsions: N/A planes: 0.865232 non-bonded: 0 chiral vol: 0.592257 rama plot: -161.74 start_pos: N/A Minimum found (iteration number 187) at -1180.47 Final Estimated RMS Z Scores: bonds: 0.150901 angles: 0.371012 torsions: N/A planes: 0.890736 non-bonded: 0 chiral vol: 0.608437 rama plot: -164.589 start_pos: N/A SUCCESS TIME:: (dragged refinement): 280.78 Refinement elapsed time: 0.028 INFO:: replace_coords: 19 atoms updated. centering on B 84 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 2 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 83 and 85 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1076.87 Initial RMS Z values bonds: 0.127601 angles: 0.374405 torsions: N/A planes: 0.783473 non-bonded: 0 chiral vol: 0.830606 rama plot: -152.232 start_pos: N/A Minimum found (iteration number 168) at -1086.45 Final Estimated RMS Z Scores: bonds: 0.120993 angles: 0.345673 torsions: N/A planes: 0.78139 non-bonded: 0 chiral vol: 0.806294 rama plot: -154.617 start_pos: N/A SUCCESS TIME:: (dragged refinement): 281.448 Refinement elapsed time: 0.083 INFO:: replace_coords: 22 atoms updated. centering on B 85 CA created 29 bond restraints created 35 angle restraints created 3 plane restraints created 3 chiral vol restraints created 70 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 84 and 86 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1153.26 Initial RMS Z values bonds: 0.133583 angles: 0.428247 torsions: N/A planes: 0.700984 non-bonded: 0.00773767 chiral vol: 0.755033 rama plot: -149.096 start_pos: N/A Minimum found (iteration number 188) at -1160.72 Final Estimated RMS Z Scores: bonds: 0.127148 angles: 0.420497 torsions: N/A planes: 0.741682 non-bonded: 8.56127e-07 chiral vol: 0.768447 rama plot: -149.127 start_pos: N/A SUCCESS TIME:: (dragged refinement): 282.174 Refinement elapsed time: 0.119 INFO:: replace_coords: 30 atoms updated. centering on B 86 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 85 and 87 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1110.31 Initial RMS Z values bonds: 0.109973 angles: 0.375166 torsions: N/A planes: 0.705246 non-bonded: 1.07977e-06 chiral vol: 0.491587 rama plot: -174.083 start_pos: N/A Minimum found (iteration number 111) at -1117.63 Final Estimated RMS Z Scores: bonds: 0.131785 angles: 0.40323 torsions: N/A planes: 0.679424 non-bonded: 3.95696e-07 chiral vol: 0.492885 rama plot: -177.651 start_pos: N/A SUCCESS TIME:: (dragged refinement): 282.87 Refinement elapsed time: 0.097 INFO:: replace_coords: 27 atoms updated. centering on B 87 CA created 22 bond restraints created 26 angle restraints created 1 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 86 and 88 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1159.81 Initial RMS Z values bonds: 0.125802 angles: 0.387372 torsions: N/A planes: 0.698188 non-bonded: 0 chiral vol: 0.326442 rama plot: -184.591 start_pos: N/A Minimum found (iteration number 296) at -1161.35 Final Estimated RMS Z Scores: bonds: 0.125203 angles: 0.380372 torsions: N/A planes: 0.663019 non-bonded: 0 chiral vol: 0.315167 rama plot: -184.675 start_pos: N/A SUCCESS TIME:: (dragged refinement): 283.428 Refinement elapsed time: 0.046 INFO:: replace_coords: 24 atoms updated. centering on B 88 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 87 and 89 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1288.95 Initial RMS Z values bonds: 0.104192 angles: 0.300494 torsions: N/A planes: 0.619245 non-bonded: 0 chiral vol: 0.0649776 rama plot: -191.609 start_pos: N/A Minimum found (iteration number 205) at -1289.28 Final Estimated RMS Z Scores: bonds: 0.108073 angles: 0.300322 torsions: N/A planes: 0.649601 non-bonded: 0 chiral vol: 0.0555706 rama plot: -191.733 start_pos: N/A SUCCESS TIME:: (dragged refinement): 284.058 Refinement elapsed time: 0.035 INFO:: replace_coords: 23 atoms updated. centering on B 89 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 4 chiral vol restraints created 52 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 88 and 90 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1328.78 Initial RMS Z values bonds: 0.125775 angles: 0.28061 torsions: N/A planes: 0.71521 non-bonded: 0 chiral vol: 0.172029 rama plot: -178.679 start_pos: N/A Minimum found (iteration number 309) at -1329.97 Final Estimated RMS Z Scores: bonds: 0.121648 angles: 0.277852 torsions: N/A planes: 0.735307 non-bonded: 0 chiral vol: 0.185231 rama plot: -178.824 start_pos: N/A SUCCESS TIME:: (dragged refinement): 284.773 Refinement elapsed time: 0.051 INFO:: replace_coords: 24 atoms updated. centering on B 90 CA created 23 bond restraints created 26 angle restraints created 1 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 89 and 91 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1326.72 Initial RMS Z values bonds: 0.144067 angles: 0.359108 torsions: N/A planes: 0.721751 non-bonded: 0 chiral vol: 0.285845 rama plot: -178.497 start_pos: N/A Minimum found (iteration number 244) at -1327.5 Final Estimated RMS Z Scores: bonds: 0.139019 angles: 0.363274 torsions: N/A planes: 0.736631 non-bonded: 0 chiral vol: 0.295093 rama plot: -178.982 start_pos: N/A SUCCESS TIME:: (dragged refinement): 285.482 Refinement elapsed time: 0.041 INFO:: replace_coords: 25 atoms updated. centering on B 91 CA created 19 bond restraints created 21 angle restraints created 0 plane restraints created 4 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 90 and 92 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1226.58 Initial RMS Z values bonds: 0.150071 angles: 0.369816 torsions: N/A planes: 0.960539 non-bonded: 0 chiral vol: 0.261384 rama plot: -177.57 start_pos: N/A Minimum found (iteration number 225) at -1226.92 Final Estimated RMS Z Scores: bonds: 0.157139 angles: 0.367621 torsions: N/A planes: 0.959591 non-bonded: 0 chiral vol: 0.243189 rama plot: -177.817 start_pos: N/A SUCCESS TIME:: (dragged refinement): 286.156 Refinement elapsed time: 0.037 INFO:: replace_coords: 22 atoms updated. centering on B 92 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 91 and 93 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1300.25 Initial RMS Z values bonds: 0.167715 angles: 0.40104 torsions: N/A planes: 0.89231 non-bonded: 0 chiral vol: 0.321719 rama plot: -174.116 start_pos: N/A Minimum found (iteration number 183) at -1301.06 Final Estimated RMS Z Scores: bonds: 0.191748 angles: 0.408722 torsions: N/A planes: 0.859471 non-bonded: 0 chiral vol: 0.332679 rama plot: -174.218 start_pos: N/A SUCCESS TIME:: (dragged refinement): 286.804 Refinement elapsed time: 0.032 INFO:: replace_coords: 24 atoms updated. centering on B 93 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 92 and 94 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1315.37 Initial RMS Z values bonds: 0.180806 angles: 0.372907 torsions: N/A planes: 0.725385 non-bonded: 0 chiral vol: 0.348888 rama plot: -173.374 start_pos: N/A Minimum found (iteration number 277) at -1318.85 Final Estimated RMS Z Scores: bonds: 0.170101 angles: 0.361321 torsions: N/A planes: 0.830334 non-bonded: 0 chiral vol: 0.342265 rama plot: -175.188 start_pos: N/A SUCCESS TIME:: (dragged refinement): 287.401 Refinement elapsed time: 0.048 INFO:: replace_coords: 25 atoms updated. centering on B 94 CA created 21 bond restraints created 24 angle restraints created 2 plane restraints created 4 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 93 and 95 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1293.24 Initial RMS Z values bonds: 0.167793 angles: 0.373222 torsions: N/A planes: 0.829225 non-bonded: 0 chiral vol: 0.422364 rama plot: -175.05 start_pos: N/A Minimum found (iteration number 291) at -1295.51 Final Estimated RMS Z Scores: bonds: 0.15436 angles: 0.393789 torsions: N/A planes: 0.789061 non-bonded: 0 chiral vol: 0.477459 rama plot: -176.158 start_pos: N/A SUCCESS TIME:: (dragged refinement): 287.973 Refinement elapsed time: 0.048 INFO:: replace_coords: 24 atoms updated. centering on B 95 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 94 and 96 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -981.144 Initial RMS Z values bonds: 0.138139 angles: 0.346065 torsions: N/A planes: 0.694536 non-bonded: 0 chiral vol: 0.4231 rama plot: -176.977 start_pos: N/A Minimum found (iteration number 293) at -982.784 Final Estimated RMS Z Scores: bonds: 0.134809 angles: 0.323283 torsions: N/A planes: 0.576103 non-bonded: 0 chiral vol: 0.409393 rama plot: -176.576 start_pos: N/A SUCCESS TIME:: (dragged refinement): 288.528 Refinement elapsed time: 0.039 INFO:: replace_coords: 22 atoms updated. centering on B 96 CA created 11 bond restraints created 12 angle restraints created 0 plane restraints created 3 chiral vol restraints created 26 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 95 and 96 of chain B Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -556.61 Initial RMS Z values bonds: 0.136318 angles: 0.351097 torsions: N/A planes: 0.114182 non-bonded: 0 chiral vol: 0.417697 rama plot: N/A start_pos: N/A Minimum found (iteration number 220) at -557.592 Final Estimated RMS Z Scores: bonds: 0.119003 angles: 0.321451 torsions: N/A planes: 0.349977 non-bonded: 0 chiral vol: 0.345347 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 289.096 Refinement elapsed time: 0.016 INFO:: replace_coords: 13 atoms updated. There are 93 residues in chain A centering on A 1 CA created 13 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -129.311 Initial RMS Z values bonds: 0.137328 angles: 0.644642 torsions: N/A planes: 1.03479 non-bonded: 0.492491 chiral vol: 0.379122 rama plot: N/A start_pos: N/A Minimum found (iteration number 28) at -202.062 Final Estimated RMS Z Scores: bonds: 0.0909695 angles: 0.511599 torsions: N/A planes: 1.08532 non-bonded: 0.00013947 chiral vol: 0.303705 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 289.757 Refinement elapsed time: 0.065 INFO:: replace_coords: 15 atoms updated. centering on A 2 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 1 and 3 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -329.293 Initial RMS Z values bonds: 0.123153 angles: 0.514669 torsions: N/A planes: 0.948637 non-bonded: 6.97348e-05 chiral vol: 0.495047 rama plot: -27.0675 start_pos: N/A Minimum found (iteration number 73) at -356.831 Final Estimated RMS Z Scores: bonds: 0.139148 angles: 0.626655 torsions: N/A planes: 1.23054 non-bonded: 0.000403925 chiral vol: 0.508968 rama plot: -52.2766 start_pos: N/A SUCCESS TIME:: (dragged refinement): 290.437 Refinement elapsed time: 0.103 INFO:: replace_coords: 21 atoms updated. centering on A 3 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 2 and 4 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -695.657 Initial RMS Z values bonds: 0.191934 angles: 0.679322 torsions: N/A planes: 1.1839 non-bonded: 0 chiral vol: 0.623013 rama plot: -114.611 start_pos: N/A Minimum found (iteration number 132) at -734.003 Final Estimated RMS Z Scores: bonds: 0.242546 angles: 0.668946 torsions: N/A planes: 0.925966 non-bonded: 0 chiral vol: 0.665289 rama plot: -129.325 start_pos: N/A SUCCESS TIME:: (dragged refinement): 290.995 Refinement elapsed time: 0.063 INFO:: replace_coords: 17 atoms updated. centering on A 4 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 3 and 5 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -939.985 Initial RMS Z values bonds: 0.246003 angles: 0.403687 torsions: N/A planes: 0.938 non-bonded: 0 chiral vol: 0.472406 rama plot: -172.797 start_pos: N/A Minimum found (iteration number 199) at -941.193 Final Estimated RMS Z Scores: bonds: 0.203783 angles: 0.384392 torsions: N/A planes: 0.919898 non-bonded: 0 chiral vol: 0.449894 rama plot: -172.744 start_pos: N/A SUCCESS TIME:: (dragged refinement): 291.541 Refinement elapsed time: 0.026 INFO:: replace_coords: 17 atoms updated. centering on A 5 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 4 and 6 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1042.2 Initial RMS Z values bonds: 0.215426 angles: 0.311287 torsions: N/A planes: 0.516952 non-bonded: 0 chiral vol: 0.158386 rama plot: -158.97 start_pos: N/A Minimum found (iteration number 226) at -1042.69 Final Estimated RMS Z Scores: bonds: 0.191794 angles: 0.29763 torsions: N/A planes: 0.49483 non-bonded: 0 chiral vol: 0.155734 rama plot: -159.077 start_pos: N/A SUCCESS TIME:: (dragged refinement): 292.167 Refinement elapsed time: 0.03 INFO:: replace_coords: 18 atoms updated. centering on A 6 CA created 17 bond restraints created 19 angle restraints created 0 plane restraints created 4 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 5 and 7 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1403.34 Initial RMS Z values bonds: 0.170905 angles: 0.266523 torsions: N/A planes: 0.474775 non-bonded: 0 chiral vol: 0.136541 rama plot: -181.89 start_pos: N/A Minimum found (iteration number 236) at -1405.13 Final Estimated RMS Z Scores: bonds: 0.176568 angles: 0.267371 torsions: N/A planes: 0.431533 non-bonded: 0 chiral vol: 0.147481 rama plot: -182.333 start_pos: N/A SUCCESS TIME:: (dragged refinement): 292.814 Refinement elapsed time: 0.033 INFO:: replace_coords: 20 atoms updated. centering on A 7 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 6 and 8 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1522.4 Initial RMS Z values bonds: 0.159778 angles: 0.18694 torsions: N/A planes: 0.391872 non-bonded: 0 chiral vol: 0.145807 rama plot: -193.424 start_pos: N/A Minimum found (iteration number 253) at -1526.42 Final Estimated RMS Z Scores: bonds: 0.210981 angles: 0.223365 torsions: N/A planes: 0.340572 non-bonded: 0 chiral vol: 0.197967 rama plot: -194.813 start_pos: N/A SUCCESS TIME:: (dragged refinement): 293.458 Refinement elapsed time: 0.037 INFO:: replace_coords: 21 atoms updated. centering on A 8 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 3 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 7 and 9 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1523.73 Initial RMS Z values bonds: 0.204327 angles: 0.322574 torsions: N/A planes: 0.276361 non-bonded: 0 chiral vol: 0.221396 rama plot: -205.394 start_pos: N/A Minimum found (iteration number 273) at -1526.68 Final Estimated RMS Z Scores: bonds: 0.182502 angles: 0.292359 torsions: N/A planes: 0.367319 non-bonded: 0 chiral vol: 0.178079 rama plot: -206.568 start_pos: N/A SUCCESS TIME:: (dragged refinement): 294.133 Refinement elapsed time: 0.039 INFO:: replace_coords: 20 atoms updated. centering on A 9 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 8 and 10 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1290.84 Initial RMS Z values bonds: 0.181475 angles: 0.355862 torsions: N/A planes: 0.506522 non-bonded: 0 chiral vol: 0.328122 rama plot: -216.998 start_pos: N/A Minimum found (iteration number 222) at -1293.26 Final Estimated RMS Z Scores: bonds: 0.206132 angles: 0.356837 torsions: N/A planes: 0.595938 non-bonded: 0 chiral vol: 0.329962 rama plot: -217.984 start_pos: N/A SUCCESS TIME:: (dragged refinement): 294.69 Refinement elapsed time: 0.032 INFO:: replace_coords: 19 atoms updated. centering on A 10 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 9 and 11 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1196.65 Initial RMS Z values bonds: 0.198814 angles: 0.414276 torsions: N/A planes: 0.722682 non-bonded: 0 chiral vol: 0.370502 rama plot: -200.278 start_pos: N/A Minimum found (iteration number 289) at -1206.54 Final Estimated RMS Z Scores: bonds: 0.233527 angles: 0.402111 torsions: N/A planes: 0.54364 non-bonded: 0 chiral vol: 0.356548 rama plot: -203.9 start_pos: N/A SUCCESS TIME:: (dragged refinement): 295.238 Refinement elapsed time: 0.04 INFO:: replace_coords: 19 atoms updated. centering on A 11 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 10 and 12 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -536.523 Initial RMS Z values bonds: 0.212065 angles: 0.399313 torsions: N/A planes: 0.719716 non-bonded: 2.22995 chiral vol: 0.354687 rama plot: -186.27 start_pos: N/A Minimum found (iteration number 2) at -1028.04 Final Estimated RMS Z Scores: bonds: 1.65808 angles: 1.18578 torsions: N/A planes: 0.819074 non-bonded: 0.117726 chiral vol: 0.380676 rama plot: -189.854 start_pos: N/A SUCCESS TIME:: (dragged refinement): 295.844 Refinement elapsed time: 0.058 INFO:: replace_coords: 20 atoms updated. centering on A 12 CA created 21 bond restraints created 24 angle restraints created 0 plane restraints created 3 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 11 and 13 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -388.541 Initial RMS Z values bonds: 1.55738 angles: 1.1306 torsions: N/A planes: 0.890538 non-bonded: 2.30261 chiral vol: 0.262994 rama plot: -181.923 start_pos: N/A Minimum found (iteration number 81) at -939.323 Final Estimated RMS Z Scores: bonds: 2.16138 angles: 1.54205 torsions: N/A planes: 0.713904 non-bonded: 0.211544 chiral vol: 0.27006 rama plot: -183.945 start_pos: N/A SUCCESS TIME:: (dragged refinement): 296.439 Refinement elapsed time: 0.07 INFO:: replace_coords: 22 atoms updated. centering on A 13 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 3 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 12 and 14 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1064.54 Initial RMS Z values bonds: 2.11925 angles: 1.51305 torsions: N/A planes: 0.585894 non-bonded: 0.0828402 chiral vol: 0.208057 rama plot: -189.018 start_pos: N/A Minimum found (iteration number 391) at -1184.5 Final Estimated RMS Z Scores: bonds: 1.50816 angles: 1.08742 torsions: N/A planes: 0.684717 non-bonded: 0.0824192 chiral vol: 0.146632 rama plot: -196.184 start_pos: N/A SUCCESS TIME:: (dragged refinement): 297.041 Refinement elapsed time: 0.059 INFO:: replace_coords: 23 atoms updated. centering on A 14 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 13 and 15 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1246.1 Initial RMS Z values bonds: 1.60262 angles: 1.12788 torsions: N/A planes: 0.595172 non-bonded: 0 chiral vol: 0.153774 rama plot: -207.809 start_pos: N/A Minimum found (iteration number 344) at -1357.66 Final Estimated RMS Z Scores: bonds: 0.176435 angles: 0.33448 torsions: N/A planes: 0.624618 non-bonded: 0 chiral vol: 0.108898 rama plot: -212.417 start_pos: N/A SUCCESS TIME:: (dragged refinement): 297.692 Refinement elapsed time: 0.05 INFO:: replace_coords: 21 atoms updated. centering on A 15 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 14 and 16 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1435.88 Initial RMS Z values bonds: 0.151546 angles: 0.22935 torsions: N/A planes: 0.39635 non-bonded: 0 chiral vol: 0.0934613 rama plot: -216.56 start_pos: N/A Minimum found (iteration number 219) at -1439.43 Final Estimated RMS Z Scores: bonds: 0.116813 angles: 0.243109 torsions: N/A planes: 0.46592 non-bonded: 0 chiral vol: 0.166333 rama plot: -218.284 start_pos: N/A SUCCESS TIME:: (dragged refinement): 298.407 Refinement elapsed time: 0.035 INFO:: replace_coords: 21 atoms updated. centering on A 16 CA created 17 bond restraints created 19 angle restraints created 1 plane restraints created 4 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 15 and 17 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1465.6 Initial RMS Z values bonds: 0.120436 angles: 0.228355 torsions: N/A planes: 0.323167 non-bonded: 0 chiral vol: 0.210793 rama plot: -219.69 start_pos: N/A Minimum found (iteration number 224) at -1468.98 Final Estimated RMS Z Scores: bonds: 0.115404 angles: 0.229626 torsions: N/A planes: 0.336972 non-bonded: 0 chiral vol: 0.186514 rama plot: -220.823 start_pos: N/A SUCCESS TIME:: (dragged refinement): 299.126 Refinement elapsed time: 0.033 INFO:: replace_coords: 20 atoms updated. centering on A 17 CA created 19 bond restraints created 22 angle restraints created 1 plane restraints created 5 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 16 and 18 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1563.29 Initial RMS Z values bonds: 0.126617 angles: 0.24826 torsions: N/A planes: 0.300389 non-bonded: 0 chiral vol: 0.169905 rama plot: -220.313 start_pos: N/A Minimum found (iteration number 193) at -1564.3 Final Estimated RMS Z Scores: bonds: 0.130511 angles: 0.25383 torsions: N/A planes: 0.264586 non-bonded: 0 chiral vol: 0.200761 rama plot: -220.499 start_pos: N/A SUCCESS TIME:: (dragged refinement): 299.84 Refinement elapsed time: 0.03 INFO:: replace_coords: 22 atoms updated. centering on A 18 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 17 and 19 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1569.16 Initial RMS Z values bonds: 0.117809 angles: 0.266138 torsions: N/A planes: 0.202494 non-bonded: 0 chiral vol: 0.22812 rama plot: -220.472 start_pos: N/A Minimum found (iteration number 160) at -1569.41 Final Estimated RMS Z Scores: bonds: 0.122449 angles: 0.276752 torsions: N/A planes: 0.187371 non-bonded: 0 chiral vol: 0.231782 rama plot: -220.514 start_pos: N/A SUCCESS TIME:: (dragged refinement): 300.557 Refinement elapsed time: 0.028 INFO:: replace_coords: 23 atoms updated. centering on A 19 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 18 and 20 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1498.82 Initial RMS Z values bonds: 0.12688 angles: 0.23704 torsions: N/A planes: 0.270565 non-bonded: 0 chiral vol: 0.150919 rama plot: -221.054 start_pos: N/A Minimum found (iteration number 238) at -1499.85 Final Estimated RMS Z Scores: bonds: 0.121382 angles: 0.221574 torsions: N/A planes: 0.288394 non-bonded: 0 chiral vol: 0.113699 rama plot: -221.393 start_pos: N/A SUCCESS TIME:: (dragged refinement): 301.352 Refinement elapsed time: 0.038 INFO:: replace_coords: 23 atoms updated. centering on A 20 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 19 and 21 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1484.73 Initial RMS Z values bonds: 0.130946 angles: 0.231546 torsions: N/A planes: 0.285796 non-bonded: 0 chiral vol: 0.145865 rama plot: -221.321 start_pos: N/A Minimum found (iteration number 250) at -1485 Final Estimated RMS Z Scores: bonds: 0.132525 angles: 0.232655 torsions: N/A planes: 0.262309 non-bonded: 0 chiral vol: 0.135999 rama plot: -221.38 start_pos: N/A SUCCESS TIME:: (dragged refinement): 302.084 Refinement elapsed time: 0.042 INFO:: replace_coords: 24 atoms updated. centering on A 21 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 20 and 22 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1461.92 Initial RMS Z values bonds: 0.132047 angles: 0.209132 torsions: N/A planes: 0.290438 non-bonded: 1.1716e-05 chiral vol: 0.125968 rama plot: -221.417 start_pos: N/A Minimum found (iteration number 235) at -1462.11 Final Estimated RMS Z Scores: bonds: 0.134532 angles: 0.209796 torsions: N/A planes: 0.272387 non-bonded: 7.98942e-06 chiral vol: 0.121032 rama plot: -221.402 start_pos: N/A SUCCESS TIME:: (dragged refinement): 302.745 Refinement elapsed time: 0.042 INFO:: replace_coords: 24 atoms updated. centering on A 22 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 4 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 21 and 23 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1358.05 Initial RMS Z values bonds: 0.13209 angles: 0.216718 torsions: N/A planes: 0.384619 non-bonded: 1.05614e-05 chiral vol: 0.126463 rama plot: -220.796 start_pos: N/A Minimum found (iteration number 210) at -1358.82 Final Estimated RMS Z Scores: bonds: 0.130033 angles: 0.206792 torsions: N/A planes: 0.417028 non-bonded: 2.36508e-05 chiral vol: 0.126352 rama plot: -221.201 start_pos: N/A SUCCESS TIME:: (dragged refinement): 303.422 Refinement elapsed time: 0.032 INFO:: replace_coords: 21 atoms updated. centering on A 23 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 4 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 22 and 24 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1212.83 Initial RMS Z values bonds: 0.119102 angles: 0.19453 torsions: N/A planes: 0.57583 non-bonded: 2.90169e-05 chiral vol: 0.0846956 rama plot: -205.698 start_pos: N/A Minimum found (iteration number 257) at -1215.52 Final Estimated RMS Z Scores: bonds: 0.113436 angles: 0.194578 torsions: N/A planes: 0.546284 non-bonded: 2.10506e-05 chiral vol: 0.102211 rama plot: -206.501 start_pos: N/A SUCCESS TIME:: (dragged refinement): 304.12 Refinement elapsed time: 0.034 INFO:: replace_coords: 19 atoms updated. centering on A 24 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 23 and 25 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1042.66 Initial RMS Z values bonds: 0.116499 angles: 0.169985 torsions: N/A planes: 0.565111 non-bonded: 0 chiral vol: 0.177035 rama plot: -181.058 start_pos: N/A Minimum found (iteration number 341) at -1050.09 Final Estimated RMS Z Scores: bonds: 0.106014 angles: 0.18818 torsions: N/A planes: 0.473254 non-bonded: 0 chiral vol: 0.177262 rama plot: -183.901 start_pos: N/A SUCCESS TIME:: (dragged refinement): 304.703 Refinement elapsed time: 0.047 INFO:: replace_coords: 19 atoms updated. centering on A 25 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 24 and 26 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -886.129 Initial RMS Z values bonds: 0.150191 angles: 0.37836 torsions: N/A planes: 0.526192 non-bonded: 0 chiral vol: 0.208538 rama plot: -149.823 start_pos: N/A Minimum found (iteration number 349) at -891.44 Final Estimated RMS Z Scores: bonds: 0.126324 angles: 0.276479 torsions: N/A planes: 0.641912 non-bonded: 0 chiral vol: 0.189327 rama plot: -150.295 start_pos: N/A SUCCESS TIME:: (dragged refinement): 305.251 Refinement elapsed time: 0.046 INFO:: replace_coords: 18 atoms updated. centering on A 26 CA created 17 bond restraints created 18 angle restraints created 1 plane restraints created 2 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 25 and 27 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -116.834 Initial RMS Z values bonds: 0.13625 angles: 0.279897 torsions: N/A planes: 0.651311 non-bonded: 3.50584 chiral vol: 0.172793 rama plot: -150.82 start_pos: N/A Minimum found (iteration number 2) at -702.198 Final Estimated RMS Z Scores: bonds: 1.87889 angles: 1.15536 torsions: N/A planes: 0.673869 non-bonded: 0.169216 chiral vol: 0.252489 rama plot: -150.193 start_pos: N/A SUCCESS TIME:: (dragged refinement): 305.825 Refinement elapsed time: 0.053 INFO:: replace_coords: 19 atoms updated. centering on A 27 CA created 21 bond restraints created 23 angle restraints created 1 plane restraints created 2 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 26 and 28 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -851.065 Initial RMS Z values bonds: 1.72136 angles: 1.06904 torsions: N/A planes: 0.569492 non-bonded: 0.100383 chiral vol: 0.216923 rama plot: -155.93 start_pos: N/A Minimum found (iteration number 342) at -855.475 Final Estimated RMS Z Scores: bonds: 1.72014 angles: 1.07199 torsions: N/A planes: 0.507216 non-bonded: 0.100654 chiral vol: 0.161275 rama plot: -157.444 start_pos: N/A SUCCESS TIME:: (dragged refinement): 306.387 Refinement elapsed time: 0.055 INFO:: replace_coords: 22 atoms updated. centering on A 28 CA created 25 bond restraints created 29 angle restraints created 1 plane restraints created 3 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 27 and 29 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -374.061 Initial RMS Z values bonds: 1.59792 angles: 0.988275 torsions: N/A planes: 0.554744 non-bonded: 1.65794 chiral vol: 0.15959 rama plot: -186.661 start_pos: N/A Minimum found (iteration number 114) at -1042.63 Final Estimated RMS Z Scores: bonds: 1.4339 angles: 1.02265 torsions: N/A planes: 0.494735 non-bonded: 0.0803437 chiral vol: 0.235585 rama plot: -189.623 start_pos: N/A SUCCESS TIME:: (dragged refinement): 307.03 Refinement elapsed time: 0.084 INFO:: replace_coords: 25 atoms updated. centering on A 29 CA created 30 bond restraints created 36 angle restraints created 2 plane restraints created 3 chiral vol restraints created 71 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 28 and 30 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1214.74 Initial RMS Z values bonds: 1.32386 angles: 0.927774 torsions: N/A planes: 0.486731 non-bonded: 0.0614393 chiral vol: 0.25131 rama plot: -188.098 start_pos: N/A Minimum found (iteration number 316) at -1221 Final Estimated RMS Z Scores: bonds: 1.33113 angles: 0.933598 torsions: N/A planes: 0.429242 non-bonded: 0.0616353 chiral vol: 0.302377 rama plot: -190.167 start_pos: N/A SUCCESS TIME:: (dragged refinement): 307.675 Refinement elapsed time: 0.066 INFO:: replace_coords: 30 atoms updated. centering on A 30 CA created 24 bond restraints created 28 angle restraints created 1 plane restraints created 3 chiral vol restraints created 56 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 29 and 31 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1106.06 Initial RMS Z values bonds: 1.46682 angles: 1.08334 torsions: N/A planes: 0.513627 non-bonded: 0 chiral vol: 0.29456 rama plot: -199.417 start_pos: N/A Minimum found (iteration number 2) at -1229.25 Final Estimated RMS Z Scores: bonds: 0.144485 angles: 0.386601 torsions: N/A planes: 0.340932 non-bonded: 0 chiral vol: 0.219109 rama plot: -204.875 start_pos: N/A SUCCESS TIME:: (dragged refinement): 308.353 Refinement elapsed time: 0.065 INFO:: replace_coords: 25 atoms updated. centering on A 31 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 30 and 32 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1140.7 Initial RMS Z values bonds: 0.10587 angles: 0.360027 torsions: N/A planes: 0.706567 non-bonded: 0 chiral vol: 0.207572 rama plot: -195.952 start_pos: N/A Minimum found (iteration number 310) at -1165.95 Final Estimated RMS Z Scores: bonds: 0.123529 angles: 0.314368 torsions: N/A planes: 0.690662 non-bonded: 0 chiral vol: 0.125396 rama plot: -204.395 start_pos: N/A SUCCESS TIME:: (dragged refinement): 309.065 Refinement elapsed time: 0.117 INFO:: replace_coords: 27 atoms updated. centering on A 32 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 3 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 31 and 33 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1062.03 Initial RMS Z values bonds: 0.145098 angles: 0.358116 torsions: N/A planes: 0.63476 non-bonded: 0.0757222 chiral vol: 0.144053 rama plot: -194.802 start_pos: N/A Minimum found (iteration number 270) at -1113.5 Final Estimated RMS Z Scores: bonds: 0.119173 angles: 0.430936 torsions: N/A planes: 0.65403 non-bonded: 0 chiral vol: 0.207512 rama plot: -201.286 start_pos: N/A SUCCESS TIME:: (dragged refinement): 309.794 Refinement elapsed time: 0.105 INFO:: replace_coords: 23 atoms updated. centering on A 33 CA created 18 bond restraints created 19 angle restraints created 2 plane restraints created 2 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 32 and 34 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1070 Initial RMS Z values bonds: 0.130064 angles: 0.515777 torsions: N/A planes: 0.739785 non-bonded: 0 chiral vol: 0.237146 rama plot: -179.526 start_pos: N/A Minimum found (iteration number 58) at -1072.92 Final Estimated RMS Z Scores: bonds: 0.126999 angles: 0.545944 torsions: N/A planes: 0.848671 non-bonded: 0 chiral vol: 0.260338 rama plot: -181.712 start_pos: N/A SUCCESS TIME:: (dragged refinement): 310.466 Refinement elapsed time: 0.066 INFO:: replace_coords: 21 atoms updated. centering on A 34 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 33 and 35 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1131.07 Initial RMS Z values bonds: 0.143478 angles: 0.393515 torsions: N/A planes: 0.819186 non-bonded: 0 chiral vol: 0.254102 rama plot: -170.544 start_pos: N/A Minimum found (iteration number 206) at -1134.39 Final Estimated RMS Z Scores: bonds: 0.155973 angles: 0.384364 torsions: N/A planes: 0.897831 non-bonded: 0 chiral vol: 0.144543 rama plot: -172.001 start_pos: N/A SUCCESS TIME:: (dragged refinement): 311.114 Refinement elapsed time: 0.03 INFO:: replace_coords: 19 atoms updated. centering on A 35 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 34 and 36 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1095.42 Initial RMS Z values bonds: 0.125576 angles: 0.365406 torsions: N/A planes: 0.867161 non-bonded: 8.89966e-06 chiral vol: 0.0927396 rama plot: -173.08 start_pos: N/A Minimum found (iteration number 165) at -1095.71 Final Estimated RMS Z Scores: bonds: 0.123053 angles: 0.363995 torsions: N/A planes: 0.835758 non-bonded: 9.7809e-06 chiral vol: 0.0674678 rama plot: -173.036 start_pos: N/A SUCCESS TIME:: (dragged refinement): 311.808 Refinement elapsed time: 0.024 INFO:: replace_coords: 18 atoms updated. centering on A 36 CA created 23 bond restraints created 27 angle restraints created 1 plane restraints created 3 chiral vol restraints created 54 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 35 and 37 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1317.87 Initial RMS Z values bonds: 0.134129 angles: 0.367481 torsions: N/A planes: 0.864849 non-bonded: 5.98943e-06 chiral vol: 0.227364 rama plot: -181.271 start_pos: N/A Minimum found (iteration number 225) at -1318.84 Final Estimated RMS Z Scores: bonds: 0.143384 angles: 0.369578 torsions: N/A planes: 0.827532 non-bonded: 8.75744e-06 chiral vol: 0.250067 rama plot: -181.707 start_pos: N/A SUCCESS TIME:: (dragged refinement): 312.531 Refinement elapsed time: 0.04 INFO:: replace_coords: 25 atoms updated. centering on A 37 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 36 and 38 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1410.87 Initial RMS Z values bonds: 0.166391 angles: 0.496721 torsions: N/A planes: 0.853951 non-bonded: 6.66164e-06 chiral vol: 0.729832 rama plot: -192.477 start_pos: N/A Minimum found (iteration number 242) at -1416.77 Final Estimated RMS Z Scores: bonds: 0.148631 angles: 0.447267 torsions: N/A planes: 0.974328 non-bonded: 3.89565e-06 chiral vol: 0.713778 rama plot: -194.322 start_pos: N/A SUCCESS TIME:: (dragged refinement): 313.295 Refinement elapsed time: 0.049 INFO:: replace_coords: 27 atoms updated. centering on A 38 CA created 26 bond restraints created 30 angle restraints created 3 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 37 and 39 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1465 Initial RMS Z values bonds: 0.158968 angles: 0.480775 torsions: N/A planes: 1.03439 non-bonded: 0 chiral vol: 0.729055 rama plot: -184.179 start_pos: N/A Minimum found (iteration number 298) at -1475.21 Final Estimated RMS Z Scores: bonds: 0.167518 angles: 0.512613 torsions: N/A planes: 0.984818 non-bonded: 0 chiral vol: 0.749181 rama plot: -184.843 start_pos: N/A SUCCESS TIME:: (dragged refinement): 314.061 Refinement elapsed time: 0.06 INFO:: replace_coords: 28 atoms updated. centering on A 39 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 38 and 40 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1354.28 Initial RMS Z values bonds: 0.249693 angles: 0.880259 torsions: N/A planes: 2.30303 non-bonded: 0 chiral vol: 1.06974 rama plot: -198.865 start_pos: N/A Minimum found (iteration number 27) at -1359.9 Final Estimated RMS Z Scores: bonds: 0.192155 angles: 0.890835 torsions: N/A planes: 2.16399 non-bonded: 0 chiral vol: 1.01452 rama plot: -198.529 start_pos: N/A SUCCESS TIME:: (dragged refinement): 314.83 Refinement elapsed time: 0.084 INFO:: replace_coords: 28 atoms updated. centering on A 40 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 39 and 41 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 4054.01 Initial RMS Z values bonds: 0.268633 angles: 1.01701 torsions: N/A planes: 2.20147 non-bonded: 9.83908 chiral vol: 0.889351 rama plot: -168.325 start_pos: N/A Minimum found (iteration number 214) at -1105.06 Final Estimated RMS Z Scores: bonds: 0.270731 angles: 1.43004 torsions: N/A planes: 2.16648 non-bonded: 0.000566335 chiral vol: 1.18386 rama plot: -178.36 start_pos: N/A SUCCESS TIME:: (dragged refinement): 315.622 Refinement elapsed time: 0.115 INFO:: replace_coords: 28 atoms updated. centering on A 41 CA created 23 bond restraints created 25 angle restraints created 2 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 40 and 42 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -917.819 Initial RMS Z values bonds: 0.269742 angles: 1.48043 torsions: N/A planes: 2.20299 non-bonded: 0.000406093 chiral vol: 1.17332 rama plot: -152.86 start_pos: N/A Minimum found (iteration number 399) at -969.271 Final Estimated RMS Z Scores: bonds: 0.266485 angles: 1.18089 torsions: N/A planes: 2.39329 non-bonded: 0.000721503 chiral vol: 1.1542 rama plot: -169.478 start_pos: N/A SUCCESS TIME:: (dragged refinement): 316.369 Refinement elapsed time: 0.07 INFO:: replace_coords: 26 atoms updated. centering on A 42 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 41 and 43 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -970.46 Initial RMS Z values bonds: 0.175398 angles: 1.05071 torsions: N/A planes: 2.49948 non-bonded: 7.67659e-05 chiral vol: 0.818875 rama plot: -168.717 start_pos: N/A Minimum found (iteration number 371) at -983.239 Final Estimated RMS Z Scores: bonds: 0.267639 angles: 0.867337 torsions: N/A planes: 2.4816 non-bonded: 0.000167318 chiral vol: 0.479511 rama plot: -169.637 start_pos: N/A SUCCESS TIME:: (dragged refinement): 317.128 Refinement elapsed time: 0.056 INFO:: replace_coords: 22 atoms updated. centering on A 43 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 42 and 44 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1235.31 Initial RMS Z values bonds: 0.150386 angles: 0.590645 torsions: N/A planes: 0.830075 non-bonded: 0 chiral vol: 0.292624 rama plot: -178.919 start_pos: N/A Minimum found (iteration number 259) at -1240.82 Final Estimated RMS Z Scores: bonds: 0.157769 angles: 0.58152 torsions: N/A planes: 0.900247 non-bonded: 0 chiral vol: 0.214861 rama plot: -182.003 start_pos: N/A SUCCESS TIME:: (dragged refinement): 317.811 Refinement elapsed time: 0.036 INFO:: replace_coords: 21 atoms updated. centering on A 44 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 3 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 43 and 45 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -691.74 Initial RMS Z values bonds: 0.15575 angles: 0.280592 torsions: N/A planes: 0.636293 non-bonded: 1.9593 chiral vol: 0.214714 rama plot: -191.09 start_pos: N/A Minimum found (iteration number 322) at -1193.03 Final Estimated RMS Z Scores: bonds: 1.57758 angles: 1.10527 torsions: N/A planes: 0.511262 non-bonded: 0.101755 chiral vol: 0.298553 rama plot: -191.617 start_pos: N/A SUCCESS TIME:: (dragged refinement): 318.548 Refinement elapsed time: 0.046 INFO:: replace_coords: 22 atoms updated. centering on A 45 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 44 and 46 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1146.99 Initial RMS Z values bonds: 1.57667 angles: 1.10725 torsions: N/A planes: 0.498267 non-bonded: 0.107741 chiral vol: 0.260434 rama plot: -177.314 start_pos: N/A Minimum found (iteration number 222) at -1149.25 Final Estimated RMS Z Scores: bonds: 1.57383 angles: 1.11726 torsions: N/A planes: 0.534342 non-bonded: 0.1074 chiral vol: 0.261197 rama plot: -178.377 start_pos: N/A SUCCESS TIME:: (dragged refinement): 319.298 Refinement elapsed time: 0.035 INFO:: replace_coords: 22 atoms updated. centering on A 46 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 45 and 47 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1212.04 Initial RMS Z values bonds: 1.54307 angles: 1.09475 torsions: N/A planes: 0.37385 non-bonded: 3.82868e-06 chiral vol: 0.117928 rama plot: -175.28 start_pos: N/A Minimum found (iteration number 358) at -1318.45 Final Estimated RMS Z Scores: bonds: 0.122394 angles: 0.315389 torsions: N/A planes: 0.477537 non-bonded: 1.69337e-06 chiral vol: 0.12338 rama plot: -176.79 start_pos: N/A SUCCESS TIME:: (dragged refinement): 320.088 Refinement elapsed time: 0.055 INFO:: replace_coords: 23 atoms updated. centering on A 47 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 46 and 48 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1286.79 Initial RMS Z values bonds: 0.122852 angles: 0.23293 torsions: N/A planes: 0.337028 non-bonded: 1.97215e-06 chiral vol: 0.138625 rama plot: -173.525 start_pos: N/A Minimum found (iteration number 240) at -1290.83 Final Estimated RMS Z Scores: bonds: 0.103832 angles: 0.213995 torsions: N/A planes: 0.343088 non-bonded: 3.23096e-06 chiral vol: 0.106327 rama plot: -175.141 start_pos: N/A SUCCESS TIME:: (dragged refinement): 320.875 Refinement elapsed time: 0.04 INFO:: replace_coords: 22 atoms updated. centering on A 48 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 47 and 49 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1435.69 Initial RMS Z values bonds: 0.141351 angles: 0.213718 torsions: N/A planes: 0.351746 non-bonded: 2.84881e-06 chiral vol: 0.224802 rama plot: -175.274 start_pos: N/A Minimum found (iteration number 283) at -1437.88 Final Estimated RMS Z Scores: bonds: 0.144269 angles: 0.231393 torsions: N/A planes: 0.29984 non-bonded: 4.00302e-06 chiral vol: 0.252707 rama plot: -175.356 start_pos: N/A SUCCESS TIME:: (dragged refinement): 321.64 Refinement elapsed time: 0.052 INFO:: replace_coords: 27 atoms updated. centering on A 49 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 2 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 48 and 50 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1252.72 Initial RMS Z values bonds: 0.145475 angles: 0.20969 torsions: N/A planes: 0.642665 non-bonded: 0 chiral vol: 0.307163 rama plot: -172.056 start_pos: N/A Minimum found (iteration number 190) at -1254.72 Final Estimated RMS Z Scores: bonds: 0.166803 angles: 0.224446 torsions: N/A planes: 0.6416 non-bonded: 0 chiral vol: 0.347274 rama plot: -172.654 start_pos: N/A SUCCESS TIME:: (dragged refinement): 322.371 Refinement elapsed time: 0.035 INFO:: replace_coords: 22 atoms updated. centering on A 50 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 49 and 51 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1537.65 Initial RMS Z values bonds: 0.140448 angles: 0.227411 torsions: N/A planes: 0.673319 non-bonded: 0 chiral vol: 0.335968 rama plot: -185.486 start_pos: N/A Minimum found (iteration number 226) at -1540.98 Final Estimated RMS Z Scores: bonds: 0.13765 angles: 0.219356 torsions: N/A planes: 0.67189 non-bonded: 0 chiral vol: 0.261962 rama plot: -186.798 start_pos: N/A SUCCESS TIME:: (dragged refinement): 323.065 Refinement elapsed time: 0.044 INFO:: replace_coords: 28 atoms updated. centering on A 51 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 50 and 52 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1584.5 Initial RMS Z values bonds: 0.0994069 angles: 0.259598 torsions: N/A planes: 0.744565 non-bonded: 0 chiral vol: 0.178597 rama plot: -183.876 start_pos: N/A Minimum found (iteration number 212) at -1585.44 Final Estimated RMS Z Scores: bonds: 0.113696 angles: 0.260045 torsions: N/A planes: 0.720095 non-bonded: 0 chiral vol: 0.183116 rama plot: -183.932 start_pos: N/A SUCCESS TIME:: (dragged refinement): 323.758 Refinement elapsed time: 0.044 INFO:: replace_coords: 28 atoms updated. centering on A 52 CA created 34 bond restraints created 42 angle restraints created 3 plane restraints created 3 chiral vol restraints created 82 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 51 and 53 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1809.91 Initial RMS Z values bonds: 0.116661 angles: 0.239653 torsions: N/A planes: 0.880052 non-bonded: 0 chiral vol: 0.168503 rama plot: -190.999 start_pos: N/A Minimum found (iteration number 229) at -1810.34 Final Estimated RMS Z Scores: bonds: 0.119067 angles: 0.234261 torsions: N/A planes: 0.897711 non-bonded: 0 chiral vol: 0.161858 rama plot: -191.08 start_pos: N/A SUCCESS TIME:: (dragged refinement): 324.494 Refinement elapsed time: 0.058 INFO:: replace_coords: 34 atoms updated. centering on A 53 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 52 and 54 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1603.04 Initial RMS Z values bonds: 0.143328 angles: 0.273909 torsions: N/A planes: 0.761441 non-bonded: 0 chiral vol: 0.150408 rama plot: -178.506 start_pos: N/A Minimum found (iteration number 241) at -1603.84 Final Estimated RMS Z Scores: bonds: 0.133936 angles: 0.275708 torsions: N/A planes: 0.775136 non-bonded: 0 chiral vol: 0.170331 rama plot: -178.781 start_pos: N/A SUCCESS TIME:: (dragged refinement): 325.264 Refinement elapsed time: 0.05 INFO:: replace_coords: 31 atoms updated. centering on A 54 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 53 and 55 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1602.91 Initial RMS Z values bonds: 0.161916 angles: 0.207212 torsions: N/A planes: 0.692772 non-bonded: 0 chiral vol: 0.118097 rama plot: -179.494 start_pos: N/A Minimum found (iteration number 369) at -1603.97 Final Estimated RMS Z Scores: bonds: 0.156188 angles: 0.199798 torsions: N/A planes: 0.684446 non-bonded: 0 chiral vol: 0.0969502 rama plot: -179.763 start_pos: N/A SUCCESS TIME:: (dragged refinement): 326.091 Refinement elapsed time: 0.077 INFO:: replace_coords: 31 atoms updated. centering on A 55 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 54 and 56 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1514.49 Initial RMS Z values bonds: 0.16795 angles: 0.251858 torsions: N/A planes: 1.30465 non-bonded: 0 chiral vol: 0.0916678 rama plot: -181.308 start_pos: N/A Minimum found (iteration number 192) at -1514.95 Final Estimated RMS Z Scores: bonds: 0.17527 angles: 0.255851 torsions: N/A planes: 1.30775 non-bonded: 0 chiral vol: 0.0957284 rama plot: -181.668 start_pos: N/A SUCCESS TIME:: (dragged refinement): 326.841 Refinement elapsed time: 0.041 INFO:: replace_coords: 28 atoms updated. centering on A 56 CA created 24 bond restraints created 29 angle restraints created 1 plane restraints created 4 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 55 and 57 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1493.69 Initial RMS Z values bonds: 0.196231 angles: 0.426303 torsions: N/A planes: 1.33521 non-bonded: 0 chiral vol: 0.363296 rama plot: -179.207 start_pos: N/A Minimum found (iteration number 169) at -1494.46 Final Estimated RMS Z Scores: bonds: 0.211842 angles: 0.450348 torsions: N/A planes: 1.30646 non-bonded: 0 chiral vol: 0.370043 rama plot: -179.75 start_pos: N/A SUCCESS TIME:: (dragged refinement): 327.54 Refinement elapsed time: 0.032 INFO:: replace_coords: 26 atoms updated. centering on A 57 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 56 and 58 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1330.55 Initial RMS Z values bonds: 0.218876 angles: 0.501698 torsions: N/A planes: 1.44939 non-bonded: 0.000184277 chiral vol: 0.337302 rama plot: -181.404 start_pos: N/A Minimum found (iteration number 179) at -1330.96 Final Estimated RMS Z Scores: bonds: 0.199139 angles: 0.496669 torsions: N/A planes: 1.46199 non-bonded: 0.000179442 chiral vol: 0.348721 rama plot: -181.346 start_pos: N/A SUCCESS TIME:: (dragged refinement): 328.213 Refinement elapsed time: 0.03 INFO:: replace_coords: 22 atoms updated. centering on A 58 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 57 and 59 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1268.28 Initial RMS Z values bonds: 0.193171 angles: 0.600608 torsions: N/A planes: 1.52205 non-bonded: 0.000190823 chiral vol: 0.442627 rama plot: -179.186 start_pos: N/A Minimum found (iteration number 246) at -1269.96 Final Estimated RMS Z Scores: bonds: 0.201221 angles: 0.579173 torsions: N/A planes: 1.51155 non-bonded: 0.00014402 chiral vol: 0.49694 rama plot: -179.518 start_pos: N/A SUCCESS TIME:: (dragged refinement): 328.849 Refinement elapsed time: 0.038 INFO:: replace_coords: 22 atoms updated. centering on A 59 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 5 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 58 and 60 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -587.811 Initial RMS Z values bonds: 0.160495 angles: 0.459544 torsions: N/A planes: 0.913388 non-bonded: 1.86561 chiral vol: 0.387836 rama plot: -179.738 start_pos: N/A Minimum found (iteration number 322) at -1078.61 Final Estimated RMS Z Scores: bonds: 1.564 angles: 1.16172 torsions: N/A planes: 0.912886 non-bonded: 0.0952232 chiral vol: 0.296353 rama plot: -181.713 start_pos: N/A SUCCESS TIME:: (dragged refinement): 329.453 Refinement elapsed time: 0.048 INFO:: replace_coords: 22 atoms updated. centering on A 60 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 59 and 61 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -908.317 Initial RMS Z values bonds: 1.7105 angles: 1.28385 torsions: N/A planes: 0.751157 non-bonded: 0.143413 chiral vol: 0.367502 rama plot: -170.824 start_pos: N/A Minimum found (iteration number 259) at -910.523 Final Estimated RMS Z Scores: bonds: 1.71447 angles: 1.26854 torsions: N/A planes: 0.810876 non-bonded: 0.143065 chiral vol: 0.367176 rama plot: -171.557 start_pos: N/A SUCCESS TIME:: (dragged refinement): 330.011 Refinement elapsed time: 0.035 INFO:: replace_coords: 18 atoms updated. centering on A 61 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 60 and 62 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -879.133 Initial RMS Z values bonds: 1.80635 angles: 1.31174 torsions: N/A planes: 0.963952 non-bonded: 0 chiral vol: 0.155413 rama plot: -170.588 start_pos: N/A Minimum found (iteration number 274) at -981.227 Final Estimated RMS Z Scores: bonds: 0.123265 angles: 0.457672 torsions: N/A planes: 0.956304 non-bonded: 0 chiral vol: 0.221998 rama plot: -169.941 start_pos: N/A SUCCESS TIME:: (dragged refinement): 330.606 Refinement elapsed time: 0.033 INFO:: replace_coords: 16 atoms updated. centering on A 62 CA created 17 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 61 and 63 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1142.48 Initial RMS Z values bonds: 0.0936409 angles: 0.344394 torsions: N/A planes: 0.831655 non-bonded: 0 chiral vol: 0.211039 rama plot: -180.827 start_pos: N/A Minimum found (iteration number 198) at -1149.71 Final Estimated RMS Z Scores: bonds: 0.0982169 angles: 0.384886 torsions: N/A planes: 0.827493 non-bonded: 0 chiral vol: 0.191348 rama plot: -183.471 start_pos: N/A SUCCESS TIME:: (dragged refinement): 331.219 Refinement elapsed time: 0.031 INFO:: replace_coords: 20 atoms updated. centering on A 63 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 62 and 64 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1234.63 Initial RMS Z values bonds: 0.108277 angles: 0.319653 torsions: N/A planes: 0.803894 non-bonded: 0 chiral vol: 0.290359 rama plot: -180.729 start_pos: N/A Minimum found (iteration number 271) at -1237.66 Final Estimated RMS Z Scores: bonds: 0.102037 angles: 0.309254 torsions: N/A planes: 0.8094 non-bonded: 0 chiral vol: 0.283775 rama plot: -182.448 start_pos: N/A SUCCESS TIME:: (dragged refinement): 331.834 Refinement elapsed time: 0.044 INFO:: replace_coords: 23 atoms updated. centering on A 64 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 63 and 65 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1349.7 Initial RMS Z values bonds: 0.10511 angles: 0.293317 torsions: N/A planes: 0.779451 non-bonded: 0 chiral vol: 0.309411 rama plot: -188.782 start_pos: N/A Minimum found (iteration number 281) at -1354.07 Final Estimated RMS Z Scores: bonds: 0.112205 angles: 0.271099 torsions: N/A planes: 0.810403 non-bonded: 0 chiral vol: 0.276993 rama plot: -189.626 start_pos: N/A SUCCESS TIME:: (dragged refinement): 332.49 Refinement elapsed time: 0.053 INFO:: replace_coords: 29 atoms updated. centering on A 65 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 64 and 66 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1069.28 Initial RMS Z values bonds: 0.128594 angles: 0.312075 torsions: N/A planes: 0.634697 non-bonded: 0 chiral vol: 0.319804 rama plot: -156.884 start_pos: N/A Minimum found (iteration number 259) at -1071.14 Final Estimated RMS Z Scores: bonds: 0.128112 angles: 0.309377 torsions: N/A planes: 0.727735 non-bonded: 0 chiral vol: 0.331843 rama plot: -157.339 start_pos: N/A SUCCESS TIME:: (dragged refinement): 333.132 Refinement elapsed time: 0.04 INFO:: replace_coords: 22 atoms updated. centering on A 66 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 65 and 67 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1085.72 Initial RMS Z values bonds: 0.133788 angles: 0.434283 torsions: N/A planes: 0.92717 non-bonded: 0 chiral vol: 0.354113 rama plot: -162.415 start_pos: N/A Minimum found (iteration number 320) at -1088.42 Final Estimated RMS Z Scores: bonds: 0.141939 angles: 0.460209 torsions: N/A planes: 0.911132 non-bonded: 0 chiral vol: 0.376841 rama plot: -164.849 start_pos: N/A SUCCESS TIME:: (dragged refinement): 333.79 Refinement elapsed time: 0.047 INFO:: replace_coords: 22 atoms updated. centering on A 67 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 66 and 68 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1143.59 Initial RMS Z values bonds: 0.15269 angles: 0.435166 torsions: N/A planes: 0.875545 non-bonded: 0 chiral vol: 0.372905 rama plot: -156.944 start_pos: N/A Minimum found (iteration number 248) at -1147.06 Final Estimated RMS Z Scores: bonds: 0.137457 angles: 0.421935 torsions: N/A planes: 0.790584 non-bonded: 0 chiral vol: 0.356582 rama plot: -156.835 start_pos: N/A SUCCESS TIME:: (dragged refinement): 334.467 Refinement elapsed time: 0.04 INFO:: replace_coords: 22 atoms updated. centering on A 68 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 67 and 69 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1461.25 Initial RMS Z values bonds: 0.141822 angles: 0.388479 torsions: N/A planes: 1.11094 non-bonded: 0 chiral vol: 0.313508 rama plot: -173.847 start_pos: N/A Minimum found (iteration number 176) at -1461.6 Final Estimated RMS Z Scores: bonds: 0.140041 angles: 0.395015 torsions: N/A planes: 1.11463 non-bonded: 0 chiral vol: 0.319646 rama plot: -174.156 start_pos: N/A SUCCESS TIME:: (dragged refinement): 335.156 Refinement elapsed time: 0.039 INFO:: replace_coords: 29 atoms updated. centering on A 69 CA created 27 bond restraints created 30 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 68 and 70 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1541.37 Initial RMS Z values bonds: 0.174215 angles: 0.377087 torsions: N/A planes: 1.11505 non-bonded: 0.000167073 chiral vol: 0.215923 rama plot: -179.091 start_pos: N/A Minimum found (iteration number 189) at -1541.57 Final Estimated RMS Z Scores: bonds: 0.161557 angles: 0.358888 torsions: N/A planes: 1.135 non-bonded: 0.000176234 chiral vol: 0.218389 rama plot: -178.973 start_pos: N/A SUCCESS TIME:: (dragged refinement): 335.911 Refinement elapsed time: 0.042 INFO:: replace_coords: 30 atoms updated. centering on A 70 CA created 24 bond restraints created 27 angle restraints created 1 plane restraints created 5 chiral vol restraints created 57 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 69 and 71 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 3 plane links initial distortion_score: -1294.3 Initial RMS Z values bonds: 0.197417 angles: 0.408676 torsions: N/A planes: 1.09633 non-bonded: 0.000182081 chiral vol: 0.198794 rama plot: -178.641 start_pos: N/A Minimum found (iteration number 243) at -1297.89 Final Estimated RMS Z Scores: bonds: 0.150559 angles: 0.37698 torsions: N/A planes: 1.05753 non-bonded: 0.000173326 chiral vol: 0.198393 rama plot: -178.538 start_pos: N/A SUCCESS TIME:: (dragged refinement): 336.744 Refinement elapsed time: 0.043 INFO:: replace_coords: 27 atoms updated. centering on A 71 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 4 chiral vol restraints created 39 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 70 and 72 of chain A Link restraints: 1 bond links 3 angle links 3 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: 2053.4 Initial RMS Z values bonds: 0.173674 angles: 0.40499 torsions: N/A planes: 1.13881 non-bonded: 10.5537 chiral vol: 0.214365 rama plot: -183.13 start_pos: N/A Minimum found (iteration number 54) at -856.257 Final Estimated RMS Z Scores: bonds: 0.285295 angles: 0.497616 torsions: N/A planes: 1.97874 non-bonded: 0.00115276 chiral vol: 0.226845 rama plot: -183.133 start_pos: N/A SUCCESS TIME:: (dragged refinement): 337.583 Refinement elapsed time: 0.054 INFO:: replace_coords: 20 atoms updated. centering on A 72 CA created 13 bond restraints created 12 angle restraints created 0 plane restraints created 2 chiral vol restraints created 27 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 71 and 73 of chain A Link restraints: 1 bond links 3 angle links 3 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -727.191 Initial RMS Z values bonds: 0.270808 angles: 0.406155 torsions: N/A planes: 1.73776 non-bonded: 0.00154613 chiral vol: 0.246184 rama plot: -165.186 start_pos: N/A Minimum found (iteration number 255) at -741.196 Final Estimated RMS Z Scores: bonds: 0.249179 angles: 0.650648 torsions: N/A planes: 1.10473 non-bonded: 0.000926069 chiral vol: 0.224844 rama plot: -175.63 start_pos: N/A SUCCESS TIME:: (dragged refinement): 338.385 Refinement elapsed time: 0.027 INFO:: replace_coords: 16 atoms updated. centering on A 73 CA created 14 bond restraints created 13 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 72 and 74 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 3 plane links initial distortion_score: -929.146 Initial RMS Z values bonds: 0.186522 angles: 0.603603 torsions: N/A planes: 1.05967 non-bonded: 0 chiral vol: 0.466061 rama plot: -190.401 start_pos: N/A Minimum found (iteration number 12) at -957.19 Final Estimated RMS Z Scores: bonds: 0.158112 angles: 0.303047 torsions: N/A planes: 0.623012 non-bonded: 0 chiral vol: 0.377899 rama plot: -196.279 start_pos: N/A SUCCESS TIME:: (dragged refinement): 339.148 Refinement elapsed time: 0.047 INFO:: replace_coords: 17 atoms updated. centering on A 74 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 73 and 75 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1169.31 Initial RMS Z values bonds: 0.138162 angles: 0.295682 torsions: N/A planes: 0.598529 non-bonded: 0 chiral vol: 0.284347 rama plot: -189.366 start_pos: N/A Minimum found (iteration number 242) at -1172.8 Final Estimated RMS Z Scores: bonds: 0.147881 angles: 0.303764 torsions: N/A planes: 0.54379 non-bonded: 0 chiral vol: 0.357042 rama plot: -190.885 start_pos: N/A SUCCESS TIME:: (dragged refinement): 339.812 Refinement elapsed time: 0.034 INFO:: replace_coords: 18 atoms updated. centering on A 75 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 74 and 76 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1254.03 Initial RMS Z values bonds: 0.164635 angles: 0.283474 torsions: N/A planes: 0.716737 non-bonded: 0 chiral vol: 0.344318 rama plot: -189.901 start_pos: N/A Minimum found (iteration number 250) at -1259.8 Final Estimated RMS Z Scores: bonds: 0.161352 angles: 0.302539 torsions: N/A planes: 0.658313 non-bonded: 0 chiral vol: 0.346729 rama plot: -192.283 start_pos: N/A SUCCESS TIME:: (dragged refinement): 340.528 Refinement elapsed time: 0.036 INFO:: replace_coords: 21 atoms updated. centering on A 76 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 75 and 77 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1194.21 Initial RMS Z values bonds: 0.153905 angles: 0.373927 torsions: N/A planes: 0.572672 non-bonded: 0 chiral vol: 0.287773 rama plot: -169.303 start_pos: N/A Minimum found (iteration number 308) at -1198.73 Final Estimated RMS Z Scores: bonds: 0.145466 angles: 0.388681 torsions: N/A planes: 0.559646 non-bonded: 0 chiral vol: 0.332857 rama plot: -169.935 start_pos: N/A SUCCESS TIME:: (dragged refinement): 341.292 Refinement elapsed time: 0.049 INFO:: replace_coords: 21 atoms updated. centering on A 77 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 76 and 78 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1370.42 Initial RMS Z values bonds: 0.147934 angles: 0.374366 torsions: N/A planes: 0.463776 non-bonded: 0 chiral vol: 0.326328 rama plot: -159.16 start_pos: N/A Minimum found (iteration number 318) at -1374.47 Final Estimated RMS Z Scores: bonds: 0.160196 angles: 0.35756 torsions: N/A planes: 0.428494 non-bonded: 0 chiral vol: 0.257903 rama plot: -160.863 start_pos: N/A SUCCESS TIME:: (dragged refinement): 342.119 Refinement elapsed time: 0.055 INFO:: replace_coords: 25 atoms updated. centering on A 78 CA created 23 bond restraints created 26 angle restraints created 3 plane restraints created 3 chiral vol restraints created 55 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 77 and 79 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1482.35 Initial RMS Z values bonds: 0.171318 angles: 0.330344 torsions: N/A planes: 0.425122 non-bonded: 0 chiral vol: 0.130957 rama plot: -159.689 start_pos: N/A Minimum found (iteration number 291) at -1486.46 Final Estimated RMS Z Scores: bonds: 0.175764 angles: 0.312377 torsions: N/A planes: 0.530293 non-bonded: 0 chiral vol: 0.155165 rama plot: -160.29 start_pos: N/A SUCCESS TIME:: (dragged refinement): 342.956 Refinement elapsed time: 0.053 INFO:: replace_coords: 26 atoms updated. centering on A 79 CA created 27 bond restraints created 32 angle restraints created 3 plane restraints created 3 chiral vol restraints created 65 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 78 and 80 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1687.92 Initial RMS Z values bonds: 0.181026 angles: 0.273594 torsions: N/A planes: 0.324022 non-bonded: 0 chiral vol: 0.0376418 rama plot: -168.062 start_pos: N/A Minimum found (iteration number 183) at -1688.96 Final Estimated RMS Z Scores: bonds: 0.165422 angles: 0.275604 torsions: N/A planes: 0.291705 non-bonded: 0 chiral vol: 0.0540131 rama plot: -168.625 start_pos: N/A SUCCESS TIME:: (dragged refinement): 343.797 Refinement elapsed time: 0.042 INFO:: replace_coords: 29 atoms updated. centering on A 80 CA created 31 bond restraints created 38 angle restraints created 3 plane restraints created 3 chiral vol restraints created 75 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 79 and 81 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1726.34 Initial RMS Z values bonds: 0.160642 angles: 0.175079 torsions: N/A planes: 0.686911 non-bonded: 0 chiral vol: 0.127842 rama plot: -179.008 start_pos: N/A Minimum found (iteration number 209) at -1727.65 Final Estimated RMS Z Scores: bonds: 0.159319 angles: 0.173428 torsions: N/A planes: 0.756731 non-bonded: 0 chiral vol: 0.122538 rama plot: -179.383 start_pos: N/A SUCCESS TIME:: (dragged refinement): 344.618 Refinement elapsed time: 0.046 INFO:: replace_coords: 32 atoms updated. centering on A 81 CA created 30 bond restraints created 37 angle restraints created 2 plane restraints created 4 chiral vol restraints created 73 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 80 and 82 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1644.07 Initial RMS Z values bonds: 0.128318 angles: 0.165161 torsions: N/A planes: 0.856318 non-bonded: 0 chiral vol: 0.113211 rama plot: -180.269 start_pos: N/A Minimum found (iteration number 204) at -1646.25 Final Estimated RMS Z Scores: bonds: 0.13571 angles: 0.17531 torsions: N/A planes: 0.835473 non-bonded: 0 chiral vol: 0.0943934 rama plot: -180.992 start_pos: N/A SUCCESS TIME:: (dragged refinement): 345.41 Refinement elapsed time: 0.043 INFO:: replace_coords: 31 atoms updated. centering on A 82 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 81 and 83 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1350.03 Initial RMS Z values bonds: 0.131798 angles: 0.193933 torsions: N/A planes: 0.943997 non-bonded: 0 chiral vol: 0.105805 rama plot: -177.428 start_pos: N/A Minimum found (iteration number 212) at -1352.71 Final Estimated RMS Z Scores: bonds: 0.117238 angles: 0.177481 torsions: N/A planes: 0.897247 non-bonded: 0 chiral vol: 0.122765 rama plot: -178.205 start_pos: N/A SUCCESS TIME:: (dragged refinement): 346.131 Refinement elapsed time: 0.036 INFO:: replace_coords: 23 atoms updated. centering on A 83 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 82 and 84 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1200.48 Initial RMS Z values bonds: 0.163717 angles: 0.370588 torsions: N/A planes: 0.886728 non-bonded: 0 chiral vol: 0.610734 rama plot: -162.136 start_pos: N/A Minimum found (iteration number 191) at -1205.55 Final Estimated RMS Z Scores: bonds: 0.160394 angles: 0.390914 torsions: N/A planes: 0.889127 non-bonded: 0 chiral vol: 0.618774 rama plot: -164.723 start_pos: N/A SUCCESS TIME:: (dragged refinement): 346.765 Refinement elapsed time: 0.029 INFO:: replace_coords: 19 atoms updated. centering on A 84 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 2 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 83 and 85 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1142.96 Initial RMS Z values bonds: 0.160482 angles: 0.420313 torsions: N/A planes: 0.795908 non-bonded: 0 chiral vol: 0.880559 rama plot: -151.186 start_pos: N/A Minimum found (iteration number 357) at -1151.43 Final Estimated RMS Z Scores: bonds: 0.149846 angles: 0.395486 torsions: N/A planes: 0.820335 non-bonded: 0 chiral vol: 0.863159 rama plot: -153.624 start_pos: N/A SUCCESS TIME:: (dragged refinement): 347.415 Refinement elapsed time: 0.054 INFO:: replace_coords: 22 atoms updated. centering on A 85 CA created 29 bond restraints created 35 angle restraints created 3 plane restraints created 3 chiral vol restraints created 70 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 84 and 86 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1326.94 Initial RMS Z values bonds: 0.149238 angles: 0.460037 torsions: N/A planes: 0.737927 non-bonded: 0.000612019 chiral vol: 0.765178 rama plot: -148.12 start_pos: N/A Minimum found (iteration number 328) at -1330.97 Final Estimated RMS Z Scores: bonds: 0.148173 angles: 0.448057 torsions: N/A planes: 0.783118 non-bonded: 0 chiral vol: 0.772027 rama plot: -148.255 start_pos: N/A SUCCESS TIME:: (dragged refinement): 348.161 Refinement elapsed time: 0.073 INFO:: replace_coords: 30 atoms updated. centering on A 86 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 85 and 87 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1242.17 Initial RMS Z values bonds: 0.128595 angles: 0.407587 torsions: N/A planes: 0.766908 non-bonded: 0 chiral vol: 0.494756 rama plot: -171.129 start_pos: N/A Minimum found (iteration number 10) at -1252.1 Final Estimated RMS Z Scores: bonds: 0.13798 angles: 0.428763 torsions: N/A planes: 0.755212 non-bonded: 0 chiral vol: 0.488568 rama plot: -176.273 start_pos: N/A SUCCESS TIME:: (dragged refinement): 348.893 Refinement elapsed time: 0.077 INFO:: replace_coords: 27 atoms updated. centering on A 87 CA created 22 bond restraints created 26 angle restraints created 1 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 86 and 88 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1236.86 Initial RMS Z values bonds: 0.119219 angles: 0.404855 torsions: N/A planes: 0.769635 non-bonded: 0 chiral vol: 0.289896 rama plot: -183.857 start_pos: N/A Minimum found (iteration number 255) at -1239.22 Final Estimated RMS Z Scores: bonds: 0.138149 angles: 0.410404 torsions: N/A planes: 0.709361 non-bonded: 0 chiral vol: 0.297924 rama plot: -183.788 start_pos: N/A SUCCESS TIME:: (dragged refinement): 349.521 Refinement elapsed time: 0.041 INFO:: replace_coords: 24 atoms updated. centering on A 88 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 87 and 89 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1098.98 Initial RMS Z values bonds: 0.144315 angles: 0.3205 torsions: N/A planes: 0.556111 non-bonded: 0.000256421 chiral vol: 0.257165 rama plot: -190.538 start_pos: N/A Minimum found (iteration number 232) at -1099.46 Final Estimated RMS Z Scores: bonds: 0.143292 angles: 0.323978 torsions: N/A planes: 0.619395 non-bonded: 0.000232527 chiral vol: 0.260235 rama plot: -190.915 start_pos: N/A SUCCESS TIME:: (dragged refinement): 350.167 Refinement elapsed time: 0.094 INFO:: replace_coords: 23 atoms updated. centering on A 89 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 4 chiral vol restraints created 52 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 88 and 90 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1157.68 Initial RMS Z values bonds: 0.137663 angles: 0.244439 torsions: N/A planes: 0.642692 non-bonded: 0.000188406 chiral vol: 0.241262 rama plot: -177.925 start_pos: N/A Minimum found (iteration number 351) at -1159.52 Final Estimated RMS Z Scores: bonds: 0.128475 angles: 0.234658 torsions: N/A planes: 0.625734 non-bonded: 0.000213492 chiral vol: 0.242123 rama plot: -178.149 start_pos: N/A SUCCESS TIME:: (dragged refinement): 350.923 Refinement elapsed time: 0.123 INFO:: replace_coords: 24 atoms updated. centering on A 90 CA created 23 bond restraints created 26 angle restraints created 1 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 89 and 91 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1190.69 Initial RMS Z values bonds: 0.139568 angles: 0.326019 torsions: N/A planes: 0.598967 non-bonded: 0.000202092 chiral vol: 0.388078 rama plot: -178.259 start_pos: N/A Minimum found (iteration number 364) at -1192.25 Final Estimated RMS Z Scores: bonds: 0.146542 angles: 0.344667 torsions: N/A planes: 0.663472 non-bonded: 0.000197917 chiral vol: 0.410834 rama plot: -179.428 start_pos: N/A SUCCESS TIME:: (dragged refinement): 351.632 Refinement elapsed time: 0.063 INFO:: replace_coords: 25 atoms updated. centering on A 91 CA created 19 bond restraints created 21 angle restraints created 0 plane restraints created 4 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 90 and 92 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1292.73 Initial RMS Z values bonds: 0.125887 angles: 0.325894 torsions: N/A planes: 0.711754 non-bonded: 0 chiral vol: 0.288281 rama plot: -178.576 start_pos: N/A Minimum found (iteration number 310) at -1294.47 Final Estimated RMS Z Scores: bonds: 0.127111 angles: 0.339472 torsions: N/A planes: 0.738934 non-bonded: 2.5134e-06 chiral vol: 0.296619 rama plot: -180.009 start_pos: N/A SUCCESS TIME:: (dragged refinement): 352.372 Refinement elapsed time: 0.048 INFO:: replace_coords: 22 atoms updated. centering on A 92 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 91 and 93 of chain A Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -1063.34 Initial RMS Z values bonds: 0.122439 angles: 0.322811 torsions: N/A planes: 0.613479 non-bonded: 2.1636e-06 chiral vol: 0.285491 rama plot: -176.861 start_pos: N/A Minimum found (iteration number 330) at -1065.08 Final Estimated RMS Z Scores: bonds: 0.112192 angles: 0.290261 torsions: N/A planes: 0.479839 non-bonded: 0 chiral vol: 0.253727 rama plot: -174.723 start_pos: N/A SUCCESS TIME:: (dragged refinement): 353.196 Refinement elapsed time: 0.049 INFO:: replace_coords: 24 atoms updated. centering on A 93 CA created 14 bond restraints created 16 angle restraints created 1 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 92 and 93 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -648.66 Initial RMS Z values bonds: 0.0902329 angles: 0.134064 torsions: N/A planes: 0.129831 non-bonded: 0 chiral vol: 0.074012 rama plot: N/A start_pos: N/A Minimum found (iteration number 142) at -648.906 Final Estimated RMS Z Scores: bonds: 0.0870005 angles: 0.113585 torsions: N/A planes: 0.168605 non-bonded: 0 chiral vol: 0.0407351 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 353.935 Refinement elapsed time: 0.014 INFO:: replace_coords: 16 atoms updated. There are 96 residues in chain B centering on B 1 CA created 13 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain B Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -373.89 Initial RMS Z values bonds: 0.153441 angles: 0.362324 torsions: N/A planes: 0.974952 non-bonded: 0 chiral vol: 0.293326 rama plot: N/A start_pos: N/A Minimum found (iteration number 252) at -377.255 Final Estimated RMS Z Scores: bonds: 0.110988 angles: 0.307109 torsions: N/A planes: 1.02517 non-bonded: 0 chiral vol: 0.250512 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 354.506 Refinement elapsed time: 0.023 INFO:: replace_coords: 15 atoms updated. centering on B 2 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 1 and 3 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -677.09 Initial RMS Z values bonds: 0.139012 angles: 0.291459 torsions: N/A planes: 0.876739 non-bonded: 0 chiral vol: 0.295105 rama plot: -172.877 start_pos: N/A Minimum found (iteration number 5) at -684.171 Final Estimated RMS Z Scores: bonds: 0.159133 angles: 0.329661 torsions: N/A planes: 1.0361 non-bonded: 0 chiral vol: 0.301748 rama plot: -178.644 start_pos: N/A SUCCESS TIME:: (dragged refinement): 355.206 Refinement elapsed time: 0.095 INFO:: replace_coords: 21 atoms updated. centering on B 3 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 2 and 4 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -890.19 Initial RMS Z values bonds: 0.192065 angles: 0.365382 torsions: N/A planes: 1.04221 non-bonded: 0 chiral vol: 0.335477 rama plot: -159.794 start_pos: N/A Minimum found (iteration number 281) at -914.699 Final Estimated RMS Z Scores: bonds: 0.230031 angles: 0.393684 torsions: N/A planes: 0.917979 non-bonded: 0 chiral vol: 0.372866 rama plot: -170.743 start_pos: N/A SUCCESS TIME:: (dragged refinement): 355.851 Refinement elapsed time: 0.035 INFO:: replace_coords: 17 atoms updated. centering on B 4 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 3 and 5 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -920.425 Initial RMS Z values bonds: 0.220341 angles: 0.312402 torsions: N/A planes: 0.663926 non-bonded: 0 chiral vol: 0.265344 rama plot: -170.186 start_pos: N/A Minimum found (iteration number 225) at -921.303 Final Estimated RMS Z Scores: bonds: 0.186591 angles: 0.282745 torsions: N/A planes: 0.720711 non-bonded: 0 chiral vol: 0.249769 rama plot: -169.649 start_pos: N/A SUCCESS TIME:: (dragged refinement): 356.507 Refinement elapsed time: 0.029 INFO:: replace_coords: 17 atoms updated. centering on B 5 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 3 chiral vol restraints created 34 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 4 and 6 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -942.179 Initial RMS Z values bonds: 0.174005 angles: 0.279863 torsions: N/A planes: 0.659933 non-bonded: 0 chiral vol: 0.136716 rama plot: -156.945 start_pos: N/A Minimum found (iteration number 221) at -943.31 Final Estimated RMS Z Scores: bonds: 0.154716 angles: 0.266496 torsions: N/A planes: 0.565307 non-bonded: 0 chiral vol: 0.136797 rama plot: -156.819 start_pos: N/A SUCCESS TIME:: (dragged refinement): 357.163 Refinement elapsed time: 0.029 INFO:: replace_coords: 18 atoms updated. centering on B 6 CA created 17 bond restraints created 19 angle restraints created 0 plane restraints created 4 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 5 and 7 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1252.79 Initial RMS Z values bonds: 0.131157 angles: 0.220021 torsions: N/A planes: 0.582232 non-bonded: 0 chiral vol: 0.119075 rama plot: -181.048 start_pos: N/A Minimum found (iteration number 216) at -1254.12 Final Estimated RMS Z Scores: bonds: 0.128069 angles: 0.207607 torsions: N/A planes: 0.570097 non-bonded: 0 chiral vol: 0.127533 rama plot: -181.508 start_pos: N/A SUCCESS TIME:: (dragged refinement): 357.858 Refinement elapsed time: 0.03 INFO:: replace_coords: 20 atoms updated. centering on B 7 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 6 and 8 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1368.59 Initial RMS Z values bonds: 0.113255 angles: 0.231057 torsions: N/A planes: 0.473155 non-bonded: 0 chiral vol: 0.0848913 rama plot: -193.725 start_pos: N/A Minimum found (iteration number 223) at -1373.31 Final Estimated RMS Z Scores: bonds: 0.168208 angles: 0.268061 torsions: N/A planes: 0.394462 non-bonded: 0 chiral vol: 0.155347 rama plot: -195.666 start_pos: N/A SUCCESS TIME:: (dragged refinement): 358.509 Refinement elapsed time: 0.033 INFO:: replace_coords: 21 atoms updated. centering on B 8 CA created 17 bond restraints created 18 angle restraints created 0 plane restraints created 3 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 7 and 9 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1415.27 Initial RMS Z values bonds: 0.175158 angles: 0.373158 torsions: N/A planes: 0.395881 non-bonded: 0 chiral vol: 0.175084 rama plot: -205.178 start_pos: N/A Minimum found (iteration number 270) at -1419.16 Final Estimated RMS Z Scores: bonds: 0.148998 angles: 0.320548 torsions: N/A planes: 0.486478 non-bonded: 0 chiral vol: 0.107852 rama plot: -206.595 start_pos: N/A SUCCESS TIME:: (dragged refinement): 359.143 Refinement elapsed time: 0.039 INFO:: replace_coords: 20 atoms updated. centering on B 9 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 8 and 10 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1230.95 Initial RMS Z values bonds: 0.146758 angles: 0.355743 torsions: N/A planes: 0.696111 non-bonded: 0 chiral vol: 0.205569 rama plot: -216.035 start_pos: N/A Minimum found (iteration number 277) at -1234.54 Final Estimated RMS Z Scores: bonds: 0.177356 angles: 0.364637 torsions: N/A planes: 0.725642 non-bonded: 0 chiral vol: 0.209383 rama plot: -217.443 start_pos: N/A SUCCESS TIME:: (dragged refinement): 359.741 Refinement elapsed time: 0.037 INFO:: replace_coords: 19 atoms updated. centering on B 10 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 9 and 11 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1191.41 Initial RMS Z values bonds: 0.196297 angles: 0.44433 torsions: N/A planes: 0.884296 non-bonded: 0 chiral vol: 0.333262 rama plot: -201.013 start_pos: N/A Minimum found (iteration number 316) at -1202.83 Final Estimated RMS Z Scores: bonds: 0.18206 angles: 0.428069 torsions: N/A planes: 0.62558 non-bonded: 0 chiral vol: 0.285656 rama plot: -204.336 start_pos: N/A SUCCESS TIME:: (dragged refinement): 360.409 Refinement elapsed time: 0.043 INFO:: replace_coords: 19 atoms updated. centering on B 11 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 10 and 12 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -541.952 Initial RMS Z values bonds: 0.174595 angles: 0.460193 torsions: N/A planes: 0.89396 non-bonded: 2.26599 chiral vol: 0.306665 rama plot: -186.986 start_pos: N/A Minimum found (iteration number 349) at -1041.87 Final Estimated RMS Z Scores: bonds: 1.64357 angles: 1.20581 torsions: N/A planes: 1.02219 non-bonded: 0.118694 chiral vol: 0.352684 rama plot: -190.553 start_pos: N/A SUCCESS TIME:: (dragged refinement): 361.096 Refinement elapsed time: 0.049 INFO:: replace_coords: 20 atoms updated. centering on B 12 CA created 21 bond restraints created 24 angle restraints created 0 plane restraints created 3 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 11 and 13 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -382.667 Initial RMS Z values bonds: 1.54494 angles: 1.16486 torsions: N/A planes: 1.09365 non-bonded: 2.41075 chiral vol: 0.306086 rama plot: -182.929 start_pos: N/A Minimum found (iteration number 2) at -986.121 Final Estimated RMS Z Scores: bonds: 2.15341 angles: 1.56303 torsions: N/A planes: 0.948042 non-bonded: 0.207094 chiral vol: 0.356863 rama plot: -186.096 start_pos: N/A SUCCESS TIME:: (dragged refinement): 361.798 Refinement elapsed time: 0.061 INFO:: replace_coords: 22 atoms updated. centering on B 13 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 3 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 12 and 14 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1088.3 Initial RMS Z values bonds: 2.10959 angles: 1.52912 torsions: N/A planes: 0.740571 non-bonded: 0.0832429 chiral vol: 0.258814 rama plot: -186.271 start_pos: N/A Minimum found (iteration number 385) at -1215.9 Final Estimated RMS Z Scores: bonds: 1.50698 angles: 1.10259 torsions: N/A planes: 0.841994 non-bonded: 0.0829555 chiral vol: 0.217985 rama plot: -195.69 start_pos: N/A SUCCESS TIME:: (dragged refinement): 362.46 Refinement elapsed time: 0.071 INFO:: replace_coords: 23 atoms updated. centering on B 14 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 13 and 15 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1252.34 Initial RMS Z values bonds: 1.60161 angles: 1.13336 torsions: N/A planes: 0.767888 non-bonded: 0 chiral vol: 0.221519 rama plot: -205.049 start_pos: N/A Minimum found (iteration number 2) at -1370.2 Final Estimated RMS Z Scores: bonds: 0.158634 angles: 0.394653 torsions: N/A planes: 0.814353 non-bonded: 0 chiral vol: 0.151016 rama plot: -211.058 start_pos: N/A SUCCESS TIME:: (dragged refinement): 363.132 Refinement elapsed time: 0.059 INFO:: replace_coords: 21 atoms updated. centering on B 15 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 14 and 16 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1387.22 Initial RMS Z values bonds: 0.130872 angles: 0.261676 torsions: N/A planes: 0.523318 non-bonded: 0 chiral vol: 0.144523 rama plot: -215.066 start_pos: N/A Minimum found (iteration number 267) at -1390.34 Final Estimated RMS Z Scores: bonds: 0.137214 angles: 0.308893 torsions: N/A planes: 0.608304 non-bonded: 1.53729e-06 chiral vol: 0.19596 rama plot: -216.745 start_pos: N/A SUCCESS TIME:: (dragged refinement): 363.791 Refinement elapsed time: 0.039 INFO:: replace_coords: 21 atoms updated. centering on B 16 CA created 17 bond restraints created 19 angle restraints created 1 plane restraints created 4 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 15 and 17 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1362.49 Initial RMS Z values bonds: 0.163032 angles: 0.320713 torsions: N/A planes: 0.474837 non-bonded: 1.44121e-06 chiral vol: 0.300257 rama plot: -219.773 start_pos: N/A Minimum found (iteration number 301) at -1365.62 Final Estimated RMS Z Scores: bonds: 0.166123 angles: 0.319146 torsions: N/A planes: 0.481765 non-bonded: 0 chiral vol: 0.275121 rama plot: -220.91 start_pos: N/A SUCCESS TIME:: (dragged refinement): 364.37 Refinement elapsed time: 0.041 INFO:: replace_coords: 20 atoms updated. centering on B 17 CA created 19 bond restraints created 22 angle restraints created 1 plane restraints created 5 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 16 and 18 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1438.94 Initial RMS Z values bonds: 0.15827 angles: 0.289805 torsions: N/A planes: 0.44888 non-bonded: 0 chiral vol: 0.221681 rama plot: -220.706 start_pos: N/A Minimum found (iteration number 206) at -1439.77 Final Estimated RMS Z Scores: bonds: 0.151219 angles: 0.296915 torsions: N/A planes: 0.411997 non-bonded: 0 chiral vol: 0.232718 rama plot: -220.804 start_pos: N/A SUCCESS TIME:: (dragged refinement): 364.94 Refinement elapsed time: 0.032 INFO:: replace_coords: 22 atoms updated. centering on B 18 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 17 and 19 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1424.08 Initial RMS Z values bonds: 0.133835 angles: 0.284821 torsions: N/A planes: 0.269 non-bonded: 0 chiral vol: 0.254815 rama plot: -220.859 start_pos: N/A Minimum found (iteration number 216) at -1424.39 Final Estimated RMS Z Scores: bonds: 0.127251 angles: 0.287974 torsions: N/A planes: 0.244265 non-bonded: 0 chiral vol: 0.260862 rama plot: -220.945 start_pos: N/A SUCCESS TIME:: (dragged refinement): 365.56 Refinement elapsed time: 0.035 INFO:: replace_coords: 23 atoms updated. centering on B 19 CA created 20 bond restraints created 23 angle restraints created 1 plane restraints created 4 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 18 and 20 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1377.02 Initial RMS Z values bonds: 0.113093 angles: 0.158104 torsions: N/A planes: 0.319623 non-bonded: 0 chiral vol: 0.130225 rama plot: -221.125 start_pos: N/A Minimum found (iteration number 234) at -1377.83 Final Estimated RMS Z Scores: bonds: 0.109645 angles: 0.15803 torsions: N/A planes: 0.341805 non-bonded: 0 chiral vol: 0.121485 rama plot: -221.407 start_pos: N/A SUCCESS TIME:: (dragged refinement): 366.136 Refinement elapsed time: 0.038 INFO:: replace_coords: 23 atoms updated. centering on B 20 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 19 and 21 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1322.66 Initial RMS Z values bonds: 0.100753 angles: 0.191303 torsions: N/A planes: 0.327017 non-bonded: 0 chiral vol: 0.164317 rama plot: -221.332 start_pos: N/A Minimum found (iteration number 206) at -1322.96 Final Estimated RMS Z Scores: bonds: 0.103114 angles: 0.18798 torsions: N/A planes: 0.323326 non-bonded: 0 chiral vol: 0.159295 rama plot: -221.408 start_pos: N/A SUCCESS TIME:: (dragged refinement): 366.649 Refinement elapsed time: 0.035 INFO:: replace_coords: 24 atoms updated. centering on B 21 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 20 and 22 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1324.68 Initial RMS Z values bonds: 0.10805 angles: 0.17051 torsions: N/A planes: 0.337045 non-bonded: 7.85818e-07 chiral vol: 0.133416 rama plot: -221.428 start_pos: N/A Minimum found (iteration number 213) at -1324.82 Final Estimated RMS Z Scores: bonds: 0.108416 angles: 0.174823 torsions: N/A planes: 0.327744 non-bonded: 1.84172e-07 chiral vol: 0.135044 rama plot: -221.436 start_pos: N/A SUCCESS TIME:: (dragged refinement): 367.216 Refinement elapsed time: 0.036 INFO:: replace_coords: 24 atoms updated. centering on B 22 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 4 chiral vol restraints created 42 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 21 and 23 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1216.66 Initial RMS Z values bonds: 0.107822 angles: 0.169635 torsions: N/A planes: 0.285995 non-bonded: 2.41804e-07 chiral vol: 0.0945036 rama plot: -221.284 start_pos: N/A Minimum found (iteration number 213) at -1216.96 Final Estimated RMS Z Scores: bonds: 0.102153 angles: 0.16103 torsions: N/A planes: 0.303296 non-bonded: 7.80323e-07 chiral vol: 0.0937071 rama plot: -221.374 start_pos: N/A SUCCESS TIME:: (dragged refinement): 367.793 Refinement elapsed time: 0.031 INFO:: replace_coords: 21 atoms updated. centering on B 23 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 4 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 22 and 24 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1108.7 Initial RMS Z values bonds: 0.0998661 angles: 0.130781 torsions: N/A planes: 0.48169 non-bonded: 9.63928e-07 chiral vol: 0.0979145 rama plot: -206.665 start_pos: N/A Minimum found (iteration number 316) at -1111.13 Final Estimated RMS Z Scores: bonds: 0.107832 angles: 0.153691 torsions: N/A planes: 0.488667 non-bonded: 1.26534e-06 chiral vol: 0.114354 rama plot: -207.082 start_pos: N/A SUCCESS TIME:: (dragged refinement): 368.301 Refinement elapsed time: 0.041 INFO:: replace_coords: 19 atoms updated. centering on B 24 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 23 and 25 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -993.021 Initial RMS Z values bonds: 0.112533 angles: 0.206406 torsions: N/A planes: 0.520395 non-bonded: 0 chiral vol: 0.283371 rama plot: -180.814 start_pos: N/A Minimum found (iteration number 315) at -1002.79 Final Estimated RMS Z Scores: bonds: 0.118804 angles: 0.208569 torsions: N/A planes: 0.418619 non-bonded: 0 chiral vol: 0.271111 rama plot: -184.848 start_pos: N/A SUCCESS TIME:: (dragged refinement): 368.803 Refinement elapsed time: 0.042 INFO:: replace_coords: 19 atoms updated. centering on B 25 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 24 and 26 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -882.723 Initial RMS Z values bonds: 0.151004 angles: 0.408136 torsions: N/A planes: 0.568217 non-bonded: 0 chiral vol: 0.330269 rama plot: -150.786 start_pos: N/A Minimum found (iteration number 283) at -886.676 Final Estimated RMS Z Scores: bonds: 0.103853 angles: 0.333462 torsions: N/A planes: 0.651229 non-bonded: 0 chiral vol: 0.318212 rama plot: -150.929 start_pos: N/A SUCCESS TIME:: (dragged refinement): 369.379 Refinement elapsed time: 0.036 INFO:: replace_coords: 18 atoms updated. centering on B 26 CA created 17 bond restraints created 18 angle restraints created 1 plane restraints created 2 chiral vol restraints created 38 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 25 and 27 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -155.351 Initial RMS Z values bonds: 0.126065 angles: 0.354142 torsions: N/A planes: 0.7377 non-bonded: 3.51418 chiral vol: 0.328687 rama plot: -152.885 start_pos: N/A Minimum found (iteration number 382) at -774.565 Final Estimated RMS Z Scores: bonds: 1.84439 angles: 1.23718 torsions: N/A planes: 0.799948 non-bonded: 0.162767 chiral vol: 0.397213 rama plot: -152.443 start_pos: N/A SUCCESS TIME:: (dragged refinement): 369.977 Refinement elapsed time: 0.05 INFO:: replace_coords: 19 atoms updated. centering on B 27 CA created 21 bond restraints created 23 angle restraints created 1 plane restraints created 2 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 26 and 28 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -917.395 Initial RMS Z values bonds: 1.68978 angles: 1.15007 torsions: N/A planes: 0.699371 non-bonded: 0.101729 chiral vol: 0.42663 rama plot: -156.929 start_pos: N/A Minimum found (iteration number 383) at -922.134 Final Estimated RMS Z Scores: bonds: 1.69334 angles: 1.13493 torsions: N/A planes: 0.537284 non-bonded: 0.101515 chiral vol: 0.303021 rama plot: -157.062 start_pos: N/A SUCCESS TIME:: (dragged refinement): 370.612 Refinement elapsed time: 0.057 INFO:: replace_coords: 22 atoms updated. centering on B 28 CA created 25 bond restraints created 29 angle restraints created 1 plane restraints created 3 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 27 and 29 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -486.155 Initial RMS Z values bonds: 1.57169 angles: 1.03854 torsions: N/A planes: 0.670286 non-bonded: 1.67379 chiral vol: 0.309776 rama plot: -189.737 start_pos: N/A Minimum found (iteration number 78) at -1144.67 Final Estimated RMS Z Scores: bonds: 1.44279 angles: 1.03402 torsions: N/A planes: 0.775279 non-bonded: 0.0818935 chiral vol: 0.439692 rama plot: -191.015 start_pos: N/A SUCCESS TIME:: (dragged refinement): 371.29 Refinement elapsed time: 0.077 INFO:: replace_coords: 25 atoms updated. centering on B 29 CA created 30 bond restraints created 36 angle restraints created 2 plane restraints created 3 chiral vol restraints created 71 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 28 and 30 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1343.23 Initial RMS Z values bonds: 1.3325 angles: 0.933859 torsions: N/A planes: 0.643781 non-bonded: 0.0623368 chiral vol: 0.434007 rama plot: -187.258 start_pos: N/A Minimum found (iteration number 312) at -1345.95 Final Estimated RMS Z Scores: bonds: 1.33705 angles: 0.93944 torsions: N/A planes: 0.63772 non-bonded: 0.0624554 chiral vol: 0.450411 rama plot: -188.486 start_pos: N/A SUCCESS TIME:: (dragged refinement): 372.02 Refinement elapsed time: 0.06 INFO:: replace_coords: 30 atoms updated. centering on B 30 CA created 24 bond restraints created 28 angle restraints created 1 plane restraints created 3 chiral vol restraints created 56 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 29 and 31 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1322.37 Initial RMS Z values bonds: 1.47426 angles: 1.03704 torsions: N/A planes: 0.575214 non-bonded: 0 chiral vol: 0.360261 rama plot: -201.727 start_pos: N/A Minimum found (iteration number 283) at -1434.19 Final Estimated RMS Z Scores: bonds: 0.138083 angles: 0.283084 torsions: N/A planes: 0.523566 non-bonded: 0 chiral vol: 0.222884 rama plot: -204.042 start_pos: N/A SUCCESS TIME:: (dragged refinement): 372.751 Refinement elapsed time: 0.05 INFO:: replace_coords: 25 atoms updated. centering on B 31 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 30 and 32 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1416.91 Initial RMS Z values bonds: 0.123661 angles: 0.315637 torsions: N/A planes: 0.466006 non-bonded: 0 chiral vol: 0.458323 rama plot: -192.809 start_pos: N/A Minimum found (iteration number 376) at -1420.54 Final Estimated RMS Z Scores: bonds: 0.14714 angles: 0.324068 torsions: N/A planes: 0.621741 non-bonded: 0 chiral vol: 0.485745 rama plot: -197.282 start_pos: N/A SUCCESS TIME:: (dragged refinement): 373.409 Refinement elapsed time: 0.068 INFO:: replace_coords: 27 atoms updated. centering on B 32 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 3 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 31 and 33 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1369.69 Initial RMS Z values bonds: 0.159661 angles: 0.345063 torsions: N/A planes: 0.433397 non-bonded: 0 chiral vol: 0.479578 rama plot: -198.154 start_pos: N/A Minimum found (iteration number 271) at -1374.08 Final Estimated RMS Z Scores: bonds: 0.159489 angles: 0.397702 torsions: N/A planes: 0.348604 non-bonded: 0 chiral vol: 0.50647 rama plot: -197.778 start_pos: N/A SUCCESS TIME:: (dragged refinement): 374.062 Refinement elapsed time: 0.045 INFO:: replace_coords: 23 atoms updated. centering on B 33 CA created 18 bond restraints created 19 angle restraints created 2 plane restraints created 2 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 32 and 34 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1236.57 Initial RMS Z values bonds: 0.155152 angles: 0.456871 torsions: N/A planes: 0.429995 non-bonded: 0 chiral vol: 0.613647 rama plot: -177.358 start_pos: N/A Minimum found (iteration number 288) at -1238.73 Final Estimated RMS Z Scores: bonds: 0.120798 angles: 0.422752 torsions: N/A planes: 0.357817 non-bonded: 0 chiral vol: 0.555509 rama plot: -176.66 start_pos: N/A SUCCESS TIME:: (dragged refinement): 374.727 Refinement elapsed time: 0.043 INFO:: replace_coords: 21 atoms updated. centering on B 34 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 33 and 35 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1188.12 Initial RMS Z values bonds: 0.128425 angles: 0.38965 torsions: N/A planes: 0.383778 non-bonded: 0 chiral vol: 0.189246 rama plot: -173.839 start_pos: N/A Minimum found (iteration number 189) at -1189.14 Final Estimated RMS Z Scores: bonds: 0.126742 angles: 0.372291 torsions: N/A planes: 0.385649 non-bonded: 0 chiral vol: 0.15781 rama plot: -174.063 start_pos: N/A SUCCESS TIME:: (dragged refinement): 375.361 Refinement elapsed time: 0.029 INFO:: replace_coords: 19 atoms updated. centering on B 35 CA created 15 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 34 and 36 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1051.87 Initial RMS Z values bonds: 0.12221 angles: 0.358022 torsions: N/A planes: 0.557472 non-bonded: 0 chiral vol: 0.137733 rama plot: -174.429 start_pos: N/A Minimum found (iteration number 230) at -1052.37 Final Estimated RMS Z Scores: bonds: 0.111049 angles: 0.337689 torsions: N/A planes: 0.52525 non-bonded: 0 chiral vol: 0.129335 rama plot: -174.364 start_pos: N/A SUCCESS TIME:: (dragged refinement): 375.95 Refinement elapsed time: 0.03 INFO:: replace_coords: 18 atoms updated. centering on B 36 CA created 23 bond restraints created 27 angle restraints created 1 plane restraints created 3 chiral vol restraints created 54 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 35 and 37 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1223 Initial RMS Z values bonds: 0.10374 angles: 0.297545 torsions: N/A planes: 0.631006 non-bonded: 0 chiral vol: 0.196074 rama plot: -180.997 start_pos: N/A Minimum found (iteration number 202) at -1224.08 Final Estimated RMS Z Scores: bonds: 0.125618 angles: 0.315116 torsions: N/A planes: 0.560453 non-bonded: 0 chiral vol: 0.225676 rama plot: -181.478 start_pos: N/A SUCCESS TIME:: (dragged refinement): 376.501 Refinement elapsed time: 0.037 INFO:: replace_coords: 25 atoms updated. centering on B 37 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 36 and 38 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1197.78 Initial RMS Z values bonds: 0.120589 angles: 0.420237 torsions: N/A planes: 0.711986 non-bonded: 0 chiral vol: 0.736219 rama plot: -191.855 start_pos: N/A Minimum found (iteration number 14) at -1202.32 Final Estimated RMS Z Scores: bonds: 0.118744 angles: 0.399164 torsions: N/A planes: 0.799227 non-bonded: 0 chiral vol: 0.690396 rama plot: -193.65 start_pos: N/A SUCCESS TIME:: (dragged refinement): 377.132 Refinement elapsed time: 0.073 INFO:: replace_coords: 27 atoms updated. centering on B 38 CA created 26 bond restraints created 30 angle restraints created 3 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 37 and 39 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1183.73 Initial RMS Z values bonds: 0.107647 angles: 0.42562 torsions: N/A planes: 0.925632 non-bonded: 0 chiral vol: 0.70396 rama plot: -181.506 start_pos: N/A Minimum found (iteration number 99) at -1192.01 Final Estimated RMS Z Scores: bonds: 0.113652 angles: 0.462316 torsions: N/A planes: 0.830121 non-bonded: 0 chiral vol: 0.802332 rama plot: -184.186 start_pos: N/A SUCCESS TIME:: (dragged refinement): 377.74 Refinement elapsed time: 0.094 INFO:: replace_coords: 28 atoms updated. centering on B 39 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 38 and 40 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1065.41 Initial RMS Z values bonds: 0.111645 angles: 0.484847 torsions: N/A planes: 0.778749 non-bonded: 1.03415e-08 chiral vol: 0.785825 rama plot: -195.078 start_pos: N/A Minimum found (iteration number 258) at -1073.34 Final Estimated RMS Z Scores: bonds: 0.111746 angles: 0.471701 torsions: N/A planes: 0.773183 non-bonded: 7.47308e-07 chiral vol: 0.733744 rama plot: -197.324 start_pos: N/A SUCCESS TIME:: (dragged refinement): 378.392 Refinement elapsed time: 0.116 INFO:: replace_coords: 28 atoms updated. centering on B 40 CA created 25 bond restraints created 28 angle restraints created 3 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 39 and 41 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1008.4 Initial RMS Z values bonds: 0.109463 angles: 0.36113 torsions: N/A planes: 0.722905 non-bonded: 6.79322e-07 chiral vol: 0.279042 rama plot: -183.877 start_pos: N/A Minimum found (iteration number 175) at -1012.25 Final Estimated RMS Z Scores: bonds: 0.111224 angles: 0.341288 torsions: N/A planes: 0.727066 non-bonded: 4.85917e-06 chiral vol: 0.357683 rama plot: -188.159 start_pos: N/A SUCCESS TIME:: (dragged refinement): 379.18 Refinement elapsed time: 0.256 INFO:: replace_coords: 28 atoms updated. centering on B 41 CA created 23 bond restraints created 25 angle restraints created 2 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 40 and 42 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -914.129 Initial RMS Z values bonds: 0.111183 angles: 0.36879 torsions: N/A planes: 0.740523 non-bonded: 6.02021e-06 chiral vol: 0.403665 rama plot: -187.353 start_pos: N/A Minimum found (iteration number 122) at -919.15 Final Estimated RMS Z Scores: bonds: 0.0889518 angles: 0.307378 torsions: N/A planes: 0.732064 non-bonded: 3.28484e-06 chiral vol: 0.342265 rama plot: -188.107 start_pos: N/A SUCCESS TIME:: (dragged refinement): 379.817 Refinement elapsed time: 0.158 INFO:: replace_coords: 26 atoms updated. centering on B 42 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 3 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 41 and 43 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -968.958 Initial RMS Z values bonds: 0.10162 angles: 0.301468 torsions: N/A planes: 0.834016 non-bonded: 1.3165e-06 chiral vol: 0.3291 rama plot: -185.451 start_pos: N/A Minimum found (iteration number 338) at -976.107 Final Estimated RMS Z Scores: bonds: 0.0994956 angles: 0.310953 torsions: N/A planes: 0.784734 non-bonded: 1.89876e-06 chiral vol: 0.333486 rama plot: -188.179 start_pos: N/A SUCCESS TIME:: (dragged refinement): 380.395 Refinement elapsed time: 0.051 INFO:: replace_coords: 22 atoms updated. centering on B 43 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints created 41 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 42 and 44 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1056.99 Initial RMS Z values bonds: 0.112381 angles: 0.389735 torsions: N/A planes: 0.875167 non-bonded: 0 chiral vol: 0.262305 rama plot: -182.554 start_pos: N/A Minimum found (iteration number 270) at -1060.52 Final Estimated RMS Z Scores: bonds: 0.0898328 angles: 0.331543 torsions: N/A planes: 0.796794 non-bonded: 0 chiral vol: 0.210006 rama plot: -182.922 start_pos: N/A SUCCESS TIME:: (dragged refinement): 380.957 Refinement elapsed time: 0.04 INFO:: replace_coords: 21 atoms updated. centering on B 44 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 3 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 43 and 45 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -519.499 Initial RMS Z values bonds: 0.0916807 angles: 0.297274 torsions: N/A planes: 0.832177 non-bonded: 1.94248 chiral vol: 0.0675739 rama plot: -191.193 start_pos: N/A Minimum found (iteration number 373) at -1020.87 Final Estimated RMS Z Scores: bonds: 1.58021 angles: 1.10798 torsions: N/A planes: 0.792594 non-bonded: 0.0981758 chiral vol: 0.172742 rama plot: -192.098 start_pos: N/A SUCCESS TIME:: (dragged refinement): 381.586 Refinement elapsed time: 0.052 INFO:: replace_coords: 22 atoms updated. centering on B 45 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 44 and 46 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1037.81 Initial RMS Z values bonds: 1.58184 angles: 1.11031 torsions: N/A planes: 0.625364 non-bonded: 0.10392 chiral vol: 0.148743 rama plot: -179.2 start_pos: N/A Minimum found (iteration number 298) at -1038.96 Final Estimated RMS Z Scores: bonds: 1.58077 angles: 1.11386 torsions: N/A planes: 0.675 non-bonded: 0.103813 chiral vol: 0.135339 rama plot: -179.885 start_pos: N/A SUCCESS TIME:: (dragged refinement): 382.203 Refinement elapsed time: 0.044 INFO:: replace_coords: 22 atoms updated. centering on B 46 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 45 and 47 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1152.91 Initial RMS Z values bonds: 1.55001 angles: 1.09524 torsions: N/A planes: 0.366523 non-bonded: 1.4445e-05 chiral vol: 0.0911219 rama plot: -176.743 start_pos: N/A Minimum found (iteration number 309) at -1255.5 Final Estimated RMS Z Scores: bonds: 0.141864 angles: 0.349277 torsions: N/A planes: 0.441988 non-bonded: 9.6553e-06 chiral vol: 0.0951086 rama plot: -177.785 start_pos: N/A SUCCESS TIME:: (dragged refinement): 382.834 Refinement elapsed time: 0.048 INFO:: replace_coords: 23 atoms updated. centering on B 47 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 46 and 48 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1251.45 Initial RMS Z values bonds: 0.179691 angles: 0.272431 torsions: N/A planes: 0.369057 non-bonded: 1.11362e-05 chiral vol: 0.164589 rama plot: -174.825 start_pos: N/A Minimum found (iteration number 232) at -1256.36 Final Estimated RMS Z Scores: bonds: 0.142843 angles: 0.230947 torsions: N/A planes: 0.417865 non-bonded: 1.5368e-05 chiral vol: 0.13433 rama plot: -176.636 start_pos: N/A SUCCESS TIME:: (dragged refinement): 383.447 Refinement elapsed time: 0.037 INFO:: replace_coords: 22 atoms updated. centering on B 48 CA created 25 bond restraints created 29 angle restraints created 2 plane restraints created 3 chiral vol restraints created 59 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 47 and 49 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1280.44 Initial RMS Z values bonds: 0.146876 angles: 0.288841 torsions: N/A planes: 0.41128 non-bonded: 7.93779e-06 chiral vol: 0.257997 rama plot: -175.8 start_pos: N/A Minimum found (iteration number 387) at -1282.83 Final Estimated RMS Z Scores: bonds: 0.14749 angles: 0.31782 torsions: N/A planes: 0.424611 non-bonded: 1.03479e-05 chiral vol: 0.278904 rama plot: -175.979 start_pos: N/A SUCCESS TIME:: (dragged refinement): 384.077 Refinement elapsed time: 0.065 INFO:: replace_coords: 27 atoms updated. centering on B 49 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 2 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 48 and 50 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1101.85 Initial RMS Z values bonds: 0.153956 angles: 0.33234 torsions: N/A planes: 0.634927 non-bonded: 0 chiral vol: 0.321126 rama plot: -171.202 start_pos: N/A Minimum found (iteration number 295) at -1104.53 Final Estimated RMS Z Scores: bonds: 0.195372 angles: 0.348447 torsions: N/A planes: 0.631692 non-bonded: 0 chiral vol: 0.375325 rama plot: -171.972 start_pos: N/A SUCCESS TIME:: (dragged refinement): 384.613 Refinement elapsed time: 0.043 INFO:: replace_coords: 22 atoms updated. centering on B 50 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 49 and 51 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1340.83 Initial RMS Z values bonds: 0.145171 angles: 0.317004 torsions: N/A planes: 0.7496 non-bonded: 0 chiral vol: 0.324809 rama plot: -184.134 start_pos: N/A Minimum found (iteration number 363) at -1344.45 Final Estimated RMS Z Scores: bonds: 0.138469 angles: 0.305779 torsions: N/A planes: 0.729484 non-bonded: 0 chiral vol: 0.262474 rama plot: -185.616 start_pos: N/A SUCCESS TIME:: (dragged refinement): 385.146 Refinement elapsed time: 0.066 INFO:: replace_coords: 28 atoms updated. centering on B 51 CA created 27 bond restraints created 32 angle restraints created 2 plane restraints created 2 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 50 and 52 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1454.87 Initial RMS Z values bonds: 0.0969446 angles: 0.3006 torsions: N/A planes: 0.828985 non-bonded: 0 chiral vol: 0.158737 rama plot: -183.274 start_pos: N/A Minimum found (iteration number 226) at -1455.55 Final Estimated RMS Z Scores: bonds: 0.0900525 angles: 0.305914 torsions: N/A planes: 0.810395 non-bonded: 0 chiral vol: 0.170199 rama plot: -183.319 start_pos: N/A SUCCESS TIME:: (dragged refinement): 385.701 Refinement elapsed time: 0.044 INFO:: replace_coords: 28 atoms updated. centering on B 52 CA created 34 bond restraints created 42 angle restraints created 3 plane restraints created 3 chiral vol restraints created 82 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 51 and 53 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1650.4 Initial RMS Z values bonds: 0.10028 angles: 0.255143 torsions: N/A planes: 0.778965 non-bonded: 0 chiral vol: 0.159766 rama plot: -191.829 start_pos: N/A Minimum found (iteration number 238) at -1650.79 Final Estimated RMS Z Scores: bonds: 0.0903801 angles: 0.241978 torsions: N/A planes: 0.799418 non-bonded: 0 chiral vol: 0.145083 rama plot: -191.921 start_pos: N/A SUCCESS TIME:: (dragged refinement): 386.298 Refinement elapsed time: 0.057 INFO:: replace_coords: 34 atoms updated. centering on B 53 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 52 and 54 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1469.55 Initial RMS Z values bonds: 0.119102 angles: 0.284304 torsions: N/A planes: 0.684192 non-bonded: 0 chiral vol: 0.308596 rama plot: -178.031 start_pos: N/A Minimum found (iteration number 32) at -1470.15 Final Estimated RMS Z Scores: bonds: 0.129032 angles: 0.286423 torsions: N/A planes: 0.713396 non-bonded: 0 chiral vol: 0.299956 rama plot: -178.126 start_pos: N/A SUCCESS TIME:: (dragged refinement): 386.971 Refinement elapsed time: 0.085 INFO:: replace_coords: 31 atoms updated. centering on B 54 CA created 30 bond restraints created 36 angle restraints created 3 plane restraints created 3 chiral vol restraints created 72 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 53 and 55 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1498.79 Initial RMS Z values bonds: 0.177248 angles: 0.252786 torsions: N/A planes: 0.542979 non-bonded: 0 chiral vol: 0.274366 rama plot: -178.12 start_pos: N/A Minimum found (iteration number 110) at -1499.87 Final Estimated RMS Z Scores: bonds: 0.17515 angles: 0.255376 torsions: N/A planes: 0.522908 non-bonded: 0 chiral vol: 0.283124 rama plot: -178.633 start_pos: N/A SUCCESS TIME:: (dragged refinement): 387.714 Refinement elapsed time: 0.103 INFO:: replace_coords: 31 atoms updated. centering on B 55 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 54 and 56 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1496.87 Initial RMS Z values bonds: 0.195249 angles: 0.273423 torsions: N/A planes: 1.12168 non-bonded: 0 chiral vol: 0.250806 rama plot: -179.948 start_pos: N/A Minimum found (iteration number 188) at -1497.33 Final Estimated RMS Z Scores: bonds: 0.1964 angles: 0.280245 torsions: N/A planes: 1.11782 non-bonded: 0 chiral vol: 0.262169 rama plot: -180.377 start_pos: N/A SUCCESS TIME:: (dragged refinement): 388.407 Refinement elapsed time: 0.039 INFO:: replace_coords: 28 atoms updated. centering on B 56 CA created 24 bond restraints created 29 angle restraints created 1 plane restraints created 4 chiral vol restraints created 58 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 55 and 57 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1466.79 Initial RMS Z values bonds: 0.219165 angles: 0.486927 torsions: N/A planes: 1.27076 non-bonded: 0 chiral vol: 0.391917 rama plot: -177.77 start_pos: N/A Minimum found (iteration number 147) at -1467.8 Final Estimated RMS Z Scores: bonds: 0.241292 angles: 0.509524 torsions: N/A planes: 1.23385 non-bonded: 0 chiral vol: 0.40427 rama plot: -178.256 start_pos: N/A SUCCESS TIME:: (dragged refinement): 389.091 Refinement elapsed time: 0.029 INFO:: replace_coords: 26 atoms updated. centering on B 57 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 56 and 58 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1324.71 Initial RMS Z values bonds: 0.232228 angles: 0.530954 torsions: N/A planes: 1.37372 non-bonded: 6.95448e-05 chiral vol: 0.361519 rama plot: -180.203 start_pos: N/A Minimum found (iteration number 187) at -1325.26 Final Estimated RMS Z Scores: bonds: 0.229212 angles: 0.528246 torsions: N/A planes: 1.40059 non-bonded: 4.90606e-05 chiral vol: 0.362713 rama plot: -180.411 start_pos: N/A SUCCESS TIME:: (dragged refinement): 389.81 Refinement elapsed time: 0.031 INFO:: replace_coords: 22 atoms updated. centering on B 58 CA created 19 bond restraints created 22 angle restraints created 0 plane restraints created 5 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 57 and 59 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1273.64 Initial RMS Z values bonds: 0.209504 angles: 0.607418 torsions: N/A planes: 1.40186 non-bonded: 5.23919e-05 chiral vol: 0.430436 rama plot: -176.807 start_pos: N/A Minimum found (iteration number 208) at -1275.77 Final Estimated RMS Z Scores: bonds: 0.224431 angles: 0.588286 torsions: N/A planes: 1.41479 non-bonded: 4.73142e-05 chiral vol: 0.474652 rama plot: -177.658 start_pos: N/A SUCCESS TIME:: (dragged refinement): 390.529 Refinement elapsed time: 0.034 INFO:: replace_coords: 22 atoms updated. centering on B 59 CA created 20 bond restraints created 23 angle restraints created 0 plane restraints created 5 chiral vol restraints created 48 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 58 and 60 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -664.346 Initial RMS Z values bonds: 0.183744 angles: 0.440671 torsions: N/A planes: 0.803328 non-bonded: 1.8165 chiral vol: 0.335402 rama plot: -180.208 start_pos: N/A Minimum found (iteration number 342) at -1142.78 Final Estimated RMS Z Scores: bonds: 1.55403 angles: 1.16317 torsions: N/A planes: 0.762986 non-bonded: 0.0942074 chiral vol: 0.245367 rama plot: -180.793 start_pos: N/A SUCCESS TIME:: (dragged refinement): 391.234 Refinement elapsed time: 0.049 INFO:: replace_coords: 22 atoms updated. centering on B 60 CA created 16 bond restraints created 17 angle restraints created 0 plane restraints created 3 chiral vol restraints created 36 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 59 and 61 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -980.409 Initial RMS Z values bonds: 1.70023 angles: 1.27411 torsions: N/A planes: 0.719554 non-bonded: 0.144225 chiral vol: 0.315754 rama plot: -167.378 start_pos: N/A Minimum found (iteration number 214) at -984.297 Final Estimated RMS Z Scores: bonds: 1.70138 angles: 1.26413 torsions: N/A planes: 0.745758 non-bonded: 0.144238 chiral vol: 0.311714 rama plot: -169.075 start_pos: N/A SUCCESS TIME:: (dragged refinement): 391.909 Refinement elapsed time: 0.027 INFO:: replace_coords: 18 atoms updated. centering on B 61 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 2 chiral vol restraints created 30 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 60 and 62 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -899.068 Initial RMS Z values bonds: 1.79326 angles: 1.3223 torsions: N/A planes: 0.668892 non-bonded: 0 chiral vol: 0.063908 rama plot: -170.8 start_pos: N/A Minimum found (iteration number 295) at -1000.44 Final Estimated RMS Z Scores: bonds: 0.114409 angles: 0.470078 torsions: N/A planes: 0.597397 non-bonded: 0 chiral vol: 0.0969838 rama plot: -170.792 start_pos: N/A SUCCESS TIME:: (dragged refinement): 392.592 Refinement elapsed time: 0.035 INFO:: replace_coords: 16 atoms updated. centering on B 62 CA created 17 bond restraints created 17 angle restraints created 1 plane restraints created 2 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 61 and 63 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1126.78 Initial RMS Z values bonds: 0.114158 angles: 0.403499 torsions: N/A planes: 0.594625 non-bonded: 0 chiral vol: 0.203339 rama plot: -168.923 start_pos: N/A Minimum found (iteration number 241) at -1128.1 Final Estimated RMS Z Scores: bonds: 0.109858 angles: 0.382682 torsions: N/A planes: 0.649617 non-bonded: 0 chiral vol: 0.217081 rama plot: -169.322 start_pos: N/A SUCCESS TIME:: (dragged refinement): 393.269 Refinement elapsed time: 0.034 INFO:: replace_coords: 20 atoms updated. centering on B 63 CA created 20 bond restraints created 22 angle restraints created 1 plane restraints created 4 chiral vol restraints created 47 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 62 and 64 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1230.97 Initial RMS Z values bonds: 0.11355 angles: 0.33512 torsions: N/A planes: 0.652974 non-bonded: 0 chiral vol: 0.186557 rama plot: -165.07 start_pos: N/A Minimum found (iteration number 273) at -1238.04 Final Estimated RMS Z Scores: bonds: 0.135646 angles: 0.365021 torsions: N/A planes: 0.749832 non-bonded: 2.01656e-05 chiral vol: 0.166074 rama plot: -171.326 start_pos: N/A SUCCESS TIME:: (dragged refinement): 394.014 Refinement elapsed time: 0.041 INFO:: replace_coords: 23 atoms updated. centering on B 64 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 63 and 65 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1412.97 Initial RMS Z values bonds: 0.130262 angles: 0.364434 torsions: N/A planes: 0.638422 non-bonded: 1.74158e-05 chiral vol: 0.164074 rama plot: -170.461 start_pos: N/A Minimum found (iteration number 355) at -1426.1 Final Estimated RMS Z Scores: bonds: 0.134262 angles: 0.32821 torsions: N/A planes: 0.63206 non-bonded: 0 chiral vol: 0.17901 rama plot: -170.853 start_pos: N/A SUCCESS TIME:: (dragged refinement): 394.819 Refinement elapsed time: 0.064 INFO:: replace_coords: 29 atoms updated. centering on B 65 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 64 and 66 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1181.27 Initial RMS Z values bonds: 0.145335 angles: 0.340379 torsions: N/A planes: 0.747365 non-bonded: 0 chiral vol: 0.128393 rama plot: -152.3 start_pos: N/A Minimum found (iteration number 191) at -1183.98 Final Estimated RMS Z Scores: bonds: 0.128167 angles: 0.327209 torsions: N/A planes: 0.878302 non-bonded: 0 chiral vol: 0.128268 rama plot: -153.04 start_pos: N/A SUCCESS TIME:: (dragged refinement): 395.564 Refinement elapsed time: 0.031 INFO:: replace_coords: 22 atoms updated. centering on B 66 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 65 and 67 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1186.26 Initial RMS Z values bonds: 0.137539 angles: 0.407357 torsions: N/A planes: 0.966053 non-bonded: 0 chiral vol: 0.329648 rama plot: -161.364 start_pos: N/A Minimum found (iteration number 248) at -1190.55 Final Estimated RMS Z Scores: bonds: 0.162943 angles: 0.451441 torsions: N/A planes: 0.900758 non-bonded: 0 chiral vol: 0.347969 rama plot: -164.627 start_pos: N/A SUCCESS TIME:: (dragged refinement): 396.263 Refinement elapsed time: 0.038 INFO:: replace_coords: 22 atoms updated. centering on B 67 CA created 19 bond restraints created 20 angle restraints created 1 plane restraints created 3 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 66 and 68 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1252.82 Initial RMS Z values bonds: 0.16763 angles: 0.436903 torsions: N/A planes: 0.906907 non-bonded: 0 chiral vol: 0.39899 rama plot: -156.45 start_pos: N/A Minimum found (iteration number 278) at -1256.51 Final Estimated RMS Z Scores: bonds: 0.142682 angles: 0.419948 torsions: N/A planes: 0.792696 non-bonded: 0 chiral vol: 0.383441 rama plot: -156.266 start_pos: N/A SUCCESS TIME:: (dragged refinement): 396.952 Refinement elapsed time: 0.043 INFO:: replace_coords: 22 atoms updated. centering on B 68 CA created 26 bond restraints created 29 angle restraints created 2 plane restraints created 4 chiral vol restraints created 61 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 67 and 69 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1547.55 Initial RMS Z values bonds: 0.182049 angles: 0.387821 torsions: N/A planes: 1.17623 non-bonded: 0 chiral vol: 0.33207 rama plot: -173.553 start_pos: N/A Minimum found (iteration number 167) at -1547.77 Final Estimated RMS Z Scores: bonds: 0.17834 angles: 0.389906 torsions: N/A planes: 1.17409 non-bonded: 0 chiral vol: 0.332796 rama plot: -173.602 start_pos: N/A SUCCESS TIME:: (dragged refinement): 397.677 Refinement elapsed time: 0.037 INFO:: replace_coords: 29 atoms updated. centering on B 69 CA created 27 bond restraints created 30 angle restraints created 2 plane restraints created 4 chiral vol restraints created 63 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 68 and 70 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1595.61 Initial RMS Z values bonds: 0.210011 angles: 0.378222 torsions: N/A planes: 1.09887 non-bonded: 2.33929e-05 chiral vol: 0.193293 rama plot: -178.879 start_pos: N/A Minimum found (iteration number 225) at -1595.86 Final Estimated RMS Z Scores: bonds: 0.186388 angles: 0.362714 torsions: N/A planes: 1.11628 non-bonded: 3.0873e-05 chiral vol: 0.196607 rama plot: -178.817 start_pos: N/A SUCCESS TIME:: (dragged refinement): 398.406 Refinement elapsed time: 0.045 INFO:: replace_coords: 30 atoms updated. centering on B 70 CA created 24 bond restraints created 27 angle restraints created 1 plane restraints created 5 chiral vol restraints created 57 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 69 and 71 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1439.97 Initial RMS Z values bonds: 0.228253 angles: 0.402421 torsions: N/A planes: 1.10644 non-bonded: 5.41111e-05 chiral vol: 0.150054 rama plot: -179.546 start_pos: N/A Minimum found (iteration number 248) at -1440.23 Final Estimated RMS Z Scores: bonds: 0.236348 angles: 0.404542 torsions: N/A planes: 1.1149 non-bonded: 4.72825e-05 chiral vol: 0.147641 rama plot: -179.719 start_pos: N/A SUCCESS TIME:: (dragged refinement): 399.145 Refinement elapsed time: 0.046 INFO:: replace_coords: 27 atoms updated. centering on B 71 CA created 18 bond restraints created 20 angle restraints created 0 plane restraints created 5 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 70 and 72 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1202.4 Initial RMS Z values bonds: 0.244843 angles: 0.438088 torsions: N/A planes: 1.2588 non-bonded: 6.88331e-05 chiral vol: 0.163875 rama plot: -178.749 start_pos: N/A Minimum found (iteration number 297) at -1203.97 Final Estimated RMS Z Scores: bonds: 0.234412 angles: 0.441107 torsions: N/A planes: 1.19801 non-bonded: 6.75673e-05 chiral vol: 0.167082 rama plot: -179.399 start_pos: N/A SUCCESS TIME:: (dragged refinement): 399.818 Refinement elapsed time: 0.042 INFO:: replace_coords: 21 atoms updated. centering on B 72 CA created 14 bond restraints created 14 angle restraints created 0 plane restraints created 3 chiral vol restraints created 31 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 71 and 73 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1072.14 Initial RMS Z values bonds: 0.216098 angles: 0.487414 torsions: N/A planes: 0.578597 non-bonded: 5.20037e-05 chiral vol: 0.185295 rama plot: -174.082 start_pos: N/A Minimum found (iteration number 364) at -1073.48 Final Estimated RMS Z Scores: bonds: 0.232997 angles: 0.469042 torsions: N/A planes: 0.642081 non-bonded: 5.21752e-05 chiral vol: 0.186197 rama plot: -174.418 start_pos: N/A SUCCESS TIME:: (dragged refinement): 400.444 Refinement elapsed time: 0.042 INFO:: replace_coords: 17 atoms updated. centering on B 73 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 72 and 74 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1057.29 Initial RMS Z values bonds: 0.164878 angles: 0.423369 torsions: N/A planes: 0.625032 non-bonded: 0 chiral vol: 0.403449 rama plot: -185.457 start_pos: N/A Minimum found (iteration number 335) at -1062.05 Final Estimated RMS Z Scores: bonds: 0.193361 angles: 0.46577 torsions: N/A planes: 0.61186 non-bonded: 0 chiral vol: 0.340012 rama plot: -186.876 start_pos: N/A SUCCESS TIME:: (dragged refinement): 400.988 Refinement elapsed time: 0.04 INFO:: replace_coords: 18 atoms updated. centering on B 74 CA created 15 bond restraints created 15 angle restraints created 1 plane restraints created 2 chiral vol restraints created 33 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 73 and 75 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1010.48 Initial RMS Z values bonds: 0.155027 angles: 0.449567 torsions: N/A planes: 0.591241 non-bonded: 0 chiral vol: 0.324101 rama plot: -188.364 start_pos: N/A Minimum found (iteration number 289) at -1014.56 Final Estimated RMS Z Scores: bonds: 0.158426 angles: 0.43642 torsions: N/A planes: 0.629574 non-bonded: 0 chiral vol: 0.390187 rama plot: -190.182 start_pos: N/A SUCCESS TIME:: (dragged refinement): 401.503 Refinement elapsed time: 0.038 INFO:: replace_coords: 18 atoms updated. centering on B 75 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 74 and 76 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1024.55 Initial RMS Z values bonds: 0.139303 angles: 0.216484 torsions: N/A planes: 0.570244 non-bonded: 0 chiral vol: 0.290059 rama plot: -193.274 start_pos: N/A Minimum found (iteration number 312) at -1028.71 Final Estimated RMS Z Scores: bonds: 0.149557 angles: 0.232623 torsions: N/A planes: 0.478509 non-bonded: 0 chiral vol: 0.29204 rama plot: -195.071 start_pos: N/A SUCCESS TIME:: (dragged refinement): 401.994 Refinement elapsed time: 0.043 INFO:: replace_coords: 21 atoms updated. centering on B 76 CA created 18 bond restraints created 20 angle restraints created 1 plane restraints created 4 chiral vol restraints created 43 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 75 and 77 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -912.096 Initial RMS Z values bonds: 0.171827 angles: 0.254462 torsions: N/A planes: 0.430861 non-bonded: 0 chiral vol: 0.120451 rama plot: -172.016 start_pos: N/A Minimum found (iteration number 344) at -916.314 Final Estimated RMS Z Scores: bonds: 0.146477 angles: 0.261546 torsions: N/A planes: 0.41401 non-bonded: 7.23167e-06 chiral vol: 0.125629 rama plot: -172.668 start_pos: N/A SUCCESS TIME:: (dragged refinement): 402.445 Refinement elapsed time: 0.05 INFO:: replace_coords: 21 atoms updated. centering on B 77 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 76 and 78 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1075.12 Initial RMS Z values bonds: 0.180958 angles: 0.360017 torsions: N/A planes: 0.375789 non-bonded: 5.46964e-06 chiral vol: 0.147216 rama plot: -158.303 start_pos: N/A Minimum found (iteration number 382) at -1076.64 Final Estimated RMS Z Scores: bonds: 0.202708 angles: 0.377628 torsions: N/A planes: 0.326578 non-bonded: 5.09545e-06 chiral vol: 0.168605 rama plot: -158.772 start_pos: N/A SUCCESS TIME:: (dragged refinement): 402.974 Refinement elapsed time: 0.063 INFO:: replace_coords: 25 atoms updated. centering on B 78 CA created 23 bond restraints created 26 angle restraints created 3 plane restraints created 3 chiral vol restraints created 55 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 77 and 79 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1232.85 Initial RMS Z values bonds: 0.224124 angles: 0.390987 torsions: N/A planes: 0.335729 non-bonded: 0 chiral vol: 0.183086 rama plot: -158.805 start_pos: N/A Minimum found (iteration number 270) at -1234.9 Final Estimated RMS Z Scores: bonds: 0.218519 angles: 0.362245 torsions: N/A planes: 0.449244 non-bonded: 0 chiral vol: 0.162492 rama plot: -159.496 start_pos: N/A SUCCESS TIME:: (dragged refinement): 403.526 Refinement elapsed time: 0.05 INFO:: replace_coords: 26 atoms updated. centering on B 79 CA created 27 bond restraints created 32 angle restraints created 3 plane restraints created 3 chiral vol restraints created 65 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 78 and 80 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1494.65 Initial RMS Z values bonds: 0.21374 angles: 0.345616 torsions: N/A planes: 0.349761 non-bonded: 0 chiral vol: 0.17549 rama plot: -166.652 start_pos: N/A Minimum found (iteration number 227) at -1495.73 Final Estimated RMS Z Scores: bonds: 0.204937 angles: 0.352675 torsions: N/A planes: 0.334505 non-bonded: 0 chiral vol: 0.169123 rama plot: -167.19 start_pos: N/A SUCCESS TIME:: (dragged refinement): 404.159 Refinement elapsed time: 0.045 INFO:: replace_coords: 29 atoms updated. centering on B 80 CA created 31 bond restraints created 38 angle restraints created 3 plane restraints created 3 chiral vol restraints created 75 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 79 and 81 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1619.89 Initial RMS Z values bonds: 0.198442 angles: 0.25517 torsions: N/A planes: 0.695527 non-bonded: 0 chiral vol: 0.156001 rama plot: -181.056 start_pos: N/A Minimum found (iteration number 200) at -1620.28 Final Estimated RMS Z Scores: bonds: 0.202539 angles: 0.249326 torsions: N/A planes: 0.740039 non-bonded: 0 chiral vol: 0.152086 rama plot: -180.886 start_pos: N/A SUCCESS TIME:: (dragged refinement): 404.862 Refinement elapsed time: 0.041 INFO:: replace_coords: 32 atoms updated. centering on B 81 CA created 30 bond restraints created 37 angle restraints created 2 plane restraints created 4 chiral vol restraints created 73 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 80 and 82 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1610.63 Initial RMS Z values bonds: 0.181525 angles: 0.193814 torsions: N/A planes: 0.86538 non-bonded: 0 chiral vol: 0.13461 rama plot: -179.948 start_pos: N/A Minimum found (iteration number 179) at -1612.92 Final Estimated RMS Z Scores: bonds: 0.18679 angles: 0.204019 torsions: N/A planes: 0.83319 non-bonded: 0 chiral vol: 0.117208 rama plot: -180.734 start_pos: N/A SUCCESS TIME:: (dragged refinement): 405.618 Refinement elapsed time: 0.038 INFO:: replace_coords: 31 atoms updated. centering on B 82 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 3 chiral vol restraints created 49 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 81 and 83 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1356.09 Initial RMS Z values bonds: 0.179077 angles: 0.204475 torsions: N/A planes: 0.942864 non-bonded: 0 chiral vol: 0.0795721 rama plot: -177.3 start_pos: N/A Minimum found (iteration number 218) at -1358.87 Final Estimated RMS Z Scores: bonds: 0.167816 angles: 0.185638 torsions: N/A planes: 0.881676 non-bonded: 0 chiral vol: 0.0964576 rama plot: -178.047 start_pos: N/A SUCCESS TIME:: (dragged refinement): 406.357 Refinement elapsed time: 0.036 INFO:: replace_coords: 23 atoms updated. centering on B 83 CA created 16 bond restraints created 17 angle restraints created 1 plane restraints created 3 chiral vol restraints created 37 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 82 and 84 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1176.19 Initial RMS Z values bonds: 0.151466 angles: 0.340968 torsions: N/A planes: 0.857207 non-bonded: 0 chiral vol: 0.594897 rama plot: -161.833 start_pos: N/A Minimum found (iteration number 195) at -1180.47 Final Estimated RMS Z Scores: bonds: 0.151018 angles: 0.367698 torsions: N/A planes: 0.887858 non-bonded: 0 chiral vol: 0.607329 rama plot: -164.614 start_pos: N/A SUCCESS TIME:: (dragged refinement): 407.047 Refinement elapsed time: 0.029 INFO:: replace_coords: 19 atoms updated. centering on B 84 CA created 20 bond restraints created 22 angle restraints created 2 plane restraints created 2 chiral vol restraints created 46 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 83 and 85 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1077.63 Initial RMS Z values bonds: 0.129378 angles: 0.377042 torsions: N/A planes: 0.759255 non-bonded: 0 chiral vol: 0.83449 rama plot: -152.529 start_pos: N/A Minimum found (iteration number 92) at -1086.46 Final Estimated RMS Z Scores: bonds: 0.121648 angles: 0.345957 torsions: N/A planes: 0.776408 non-bonded: 0 chiral vol: 0.809896 rama plot: -154.647 start_pos: N/A SUCCESS TIME:: (dragged refinement): 407.708 Refinement elapsed time: 0.073 INFO:: replace_coords: 22 atoms updated. centering on B 85 CA created 29 bond restraints created 35 angle restraints created 3 plane restraints created 3 chiral vol restraints created 70 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 84 and 86 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1155.22 Initial RMS Z values bonds: 0.134794 angles: 0.432773 torsions: N/A planes: 0.69348 non-bonded: 0.00569462 chiral vol: 0.7532 rama plot: -149.212 start_pos: N/A Minimum found (iteration number 65) at -1160.99 Final Estimated RMS Z Scores: bonds: 0.124912 angles: 0.424133 torsions: N/A planes: 0.747253 non-bonded: 9.20802e-07 chiral vol: 0.766229 rama plot: -149.228 start_pos: N/A SUCCESS TIME:: (dragged refinement): 408.414 Refinement elapsed time: 0.098 INFO:: replace_coords: 30 atoms updated. centering on B 86 CA created 26 bond restraints created 31 angle restraints created 2 plane restraints created 3 chiral vol restraints created 62 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 85 and 87 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1111.11 Initial RMS Z values bonds: 0.108985 angles: 0.379387 torsions: N/A planes: 0.710532 non-bonded: 1.1651e-06 chiral vol: 0.486931 rama plot: -174.559 start_pos: N/A Minimum found (iteration number 165) at -1117.53 Final Estimated RMS Z Scores: bonds: 0.130522 angles: 0.403121 torsions: N/A planes: 0.676334 non-bonded: 3.41417e-07 chiral vol: 0.488971 rama plot: -177.665 start_pos: N/A SUCCESS TIME:: (dragged refinement): 409.114 Refinement elapsed time: 0.102 INFO:: replace_coords: 27 atoms updated. centering on B 87 CA created 22 bond restraints created 26 angle restraints created 1 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 86 and 88 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1159.74 Initial RMS Z values bonds: 0.123645 angles: 0.385989 torsions: N/A planes: 0.69546 non-bonded: 0 chiral vol: 0.322487 rama plot: -184.615 start_pos: N/A Minimum found (iteration number 280) at -1161.22 Final Estimated RMS Z Scores: bonds: 0.127601 angles: 0.382095 torsions: N/A planes: 0.660182 non-bonded: 0 chiral vol: 0.314598 rama plot: -184.686 start_pos: N/A SUCCESS TIME:: (dragged refinement): 409.671 Refinement elapsed time: 0.044 INFO:: replace_coords: 24 atoms updated. centering on B 88 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 87 and 89 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1288.66 Initial RMS Z values bonds: 0.106242 angles: 0.303154 torsions: N/A planes: 0.629096 non-bonded: 0 chiral vol: 0.0587772 rama plot: -191.666 start_pos: N/A Minimum found (iteration number 211) at -1288.86 Final Estimated RMS Z Scores: bonds: 0.114108 angles: 0.302551 torsions: N/A planes: 0.654289 non-bonded: 0 chiral vol: 0.0513801 rama plot: -191.756 start_pos: N/A SUCCESS TIME:: (dragged refinement): 410.301 Refinement elapsed time: 0.036 INFO:: replace_coords: 23 atoms updated. centering on B 89 CA created 22 bond restraints created 25 angle restraints created 1 plane restraints created 4 chiral vol restraints created 52 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 88 and 90 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1328.99 Initial RMS Z values bonds: 0.127938 angles: 0.277743 torsions: N/A planes: 0.712959 non-bonded: 0 chiral vol: 0.176852 rama plot: -178.674 start_pos: N/A Minimum found (iteration number 264) at -1329.99 Final Estimated RMS Z Scores: bonds: 0.122027 angles: 0.280267 torsions: N/A planes: 0.726291 non-bonded: 0 chiral vol: 0.185416 rama plot: -178.811 start_pos: N/A SUCCESS TIME:: (dragged refinement): 411.007 Refinement elapsed time: 0.044 INFO:: replace_coords: 24 atoms updated. centering on B 90 CA created 23 bond restraints created 26 angle restraints created 1 plane restraints created 3 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 89 and 91 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1326.55 Initial RMS Z values bonds: 0.143628 angles: 0.356109 torsions: N/A planes: 0.713584 non-bonded: 0 chiral vol: 0.284995 rama plot: -178.334 start_pos: N/A Minimum found (iteration number 261) at -1327.24 Final Estimated RMS Z Scores: bonds: 0.140444 angles: 0.361431 torsions: N/A planes: 0.729983 non-bonded: 0 chiral vol: 0.295567 rama plot: -178.835 start_pos: N/A SUCCESS TIME:: (dragged refinement): 411.718 Refinement elapsed time: 0.042 INFO:: replace_coords: 25 atoms updated. centering on B 91 CA created 19 bond restraints created 21 angle restraints created 0 plane restraints created 4 chiral vol restraints created 44 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 90 and 92 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1226.28 Initial RMS Z values bonds: 0.153741 angles: 0.364811 torsions: N/A planes: 0.968992 non-bonded: 0 chiral vol: 0.259685 rama plot: -177.458 start_pos: N/A Minimum found (iteration number 221) at -1226.71 Final Estimated RMS Z Scores: bonds: 0.156901 angles: 0.369025 torsions: N/A planes: 0.965931 non-bonded: 0 chiral vol: 0.242511 rama plot: -177.774 start_pos: N/A SUCCESS TIME:: (dragged refinement): 412.391 Refinement elapsed time: 0.036 INFO:: replace_coords: 22 atoms updated. centering on B 92 CA created 21 bond restraints created 24 angle restraints created 1 plane restraints created 4 chiral vol restraints created 50 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 91 and 93 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1300.17 Initial RMS Z values bonds: 0.165014 angles: 0.400876 torsions: N/A planes: 0.901665 non-bonded: 0 chiral vol: 0.323524 rama plot: -174.227 start_pos: N/A Minimum found (iteration number 171) at -1301.07 Final Estimated RMS Z Scores: bonds: 0.190817 angles: 0.406516 torsions: N/A planes: 0.864305 non-bonded: 0 chiral vol: 0.330732 rama plot: -174.255 start_pos: N/A SUCCESS TIME:: (dragged refinement): 413.038 Refinement elapsed time: 0.031 INFO:: replace_coords: 24 atoms updated. centering on B 93 CA created 22 bond restraints created 25 angle restraints created 2 plane restraints created 4 chiral vol restraints created 53 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 92 and 94 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1315.66 Initial RMS Z values bonds: 0.180025 angles: 0.369183 torsions: N/A planes: 0.730409 non-bonded: 0 chiral vol: 0.344746 rama plot: -173.494 start_pos: N/A Minimum found (iteration number 275) at -1318.9 Final Estimated RMS Z Scores: bonds: 0.169053 angles: 0.359902 torsions: N/A planes: 0.830895 non-bonded: 0 chiral vol: 0.342941 rama plot: -175.203 start_pos: N/A SUCCESS TIME:: (dragged refinement): 413.634 Refinement elapsed time: 0.048 INFO:: replace_coords: 25 atoms updated. centering on B 94 CA created 21 bond restraints created 24 angle restraints created 2 plane restraints created 4 chiral vol restraints created 51 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 93 and 95 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links initial distortion_score: -1293.24 Initial RMS Z values bonds: 0.166825 angles: 0.371374 torsions: N/A planes: 0.82983 non-bonded: 0 chiral vol: 0.421522 rama plot: -175.051 start_pos: N/A Minimum found (iteration number 269) at -1295.51 Final Estimated RMS Z Scores: bonds: 0.154658 angles: 0.39325 torsions: N/A planes: 0.788686 non-bonded: 0 chiral vol: 0.477512 rama plot: -176.162 start_pos: N/A SUCCESS TIME:: (dragged refinement): 414.204 Refinement elapsed time: 0.047 INFO:: replace_coords: 24 atoms updated. centering on B 95 CA created 19 bond restraints created 21 angle restraints created 1 plane restraints created 4 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 3 residues (for link restraints) between (and including) residues 94 and 96 of chain B Link restraints: 2 bond links 6 angle links 4 plane links 1 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -981.127 Initial RMS Z values bonds: 0.138463 angles: 0.34536 torsions: N/A planes: 0.694707 non-bonded: 0 chiral vol: 0.423095 rama plot: -176.972 start_pos: N/A Minimum found (iteration number 316) at -982.771 Final Estimated RMS Z Scores: bonds: 0.134822 angles: 0.323132 torsions: N/A planes: 0.57719 non-bonded: 0 chiral vol: 0.409225 rama plot: -176.576 start_pos: N/A SUCCESS TIME:: (dragged refinement): 414.764 Refinement elapsed time: 0.041 INFO:: replace_coords: 22 atoms updated. centering on B 96 CA created 11 bond restraints created 12 angle restraints created 0 plane restraints created 3 chiral vol restraints created 26 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 95 and 96 of chain B Link restraints: 1 bond links 3 angle links 2 plane links 0 torsion/rama links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 1 bond links 3 angle links 2 plane links initial distortion_score: -556.611 Initial RMS Z values bonds: 0.136302 angles: 0.350991 torsions: N/A planes: 0.113983 non-bonded: 0 chiral vol: 0.417605 rama plot: N/A start_pos: N/A Minimum found (iteration number 218) at -557.592 Final Estimated RMS Z Scores: bonds: 0.118905 angles: 0.321304 torsions: N/A planes: 0.349809 non-bonded: 0 chiral vol: 0.345313 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 415.331 Refinement elapsed time: 0.016 INFO:: replace_coords: 13 atoms updated. gzip: stdout: Broken pipe gzip: stdout: Broken pipe ok test99_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... Reading coordinate file: rnase_zip_test.pdb.gz PDB file rnase_zip_test.pdb.gz has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 85 read successfully DEBUG:: there were 0 types with no dictionary ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.9028 13.6977 9.2374 90 98.211 90 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 86 read successfully ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.3243 34.3243 11.0887 90 90 90 READ-INS:: Spacegroup: "I 41 2 2" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 87 read successfully INFO:: spacegroup: I 41 2 2 ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.726 77.726 77.726 90 90 90 READ-INS:: Spacegroup: "I 21 3" INFO:: chain has 121 residues Symmetry available for this molecule Molecule 88 read successfully DEBUG:: space group initialised with symbol "I 21 3" Map statistics: mean: -5.07009e-05 st.d: 0.305174 Map statistics: min: -0.781031, max: 6.07907 -0.609528 4955 -0.266523 80201 0.0764816 136171 0.419487 11448 0.762492 4907 1.1055 2959 1.4485 1483 1.79151 595 2.13451 234 2.47752 108 2.82052 34 3.16353 23 3.50653 8 3.84954 10 4.19254 7 4.53555 3 4.87855 2 5.22156 1 5.56456 0 5.90757 1 6.25057 0 Map statistics: mean: -1.00547e-05 st.d: 0.0468085 Map statistics: min: -0.211523, max: 0.648623 -0.19002 55 -0.147012 996 -0.104005 7933 -0.0609978 37110 -0.0179905 84420 0.0250169 76364 0.0680242 29138 0.111032 5797 0.154039 1047 0.197046 210 0.240053 40 0.283061 21 0.326068 4 0.369075 3 0.412083 3 0.45509 3 0.498097 2 0.541105 2 0.584112 0 0.627119 2 0.670127 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... WARNING:: invalid molecule (204050) for write_shelx_ins_file ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... Symmetry available for this molecule ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... Symmetry available for this molecule INFO:: Masking around 32 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. B 2021 ALA N :: xyz = ( -10.55, 18.01, 59.5) B 2021 ALA C :: xyz = ( -9.167, 19.73, 60.59) B 2021 ALA CA :: xyz = ( -10.5, 18.99, 60.57) B 2021 ALA O :: xyz = ( -8.111, 19.11, 60.74) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Fri_Sep_13_04:52:22_2013_modification_0.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CD2" ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Fri_Sep_13_04:52:22_2013_modification_0.res 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.305174 INFO:: Using density cut-off: 0.183104 (0.6 sigma) (mean -0.0203497 stdev: 0.111926) INFO:: Using water to protein distance limits: 1.5 3.6 Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water INFO:: found 126 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Fri_Sep_13_04:52:22_2013_modification_1.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O " INFO:: Adding to solvent chain: D ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.14 83.03 89.79 90 90 90 READ-INS:: Spacegroup: "P 21 21 21" INFO:: chain has 5 residues Symmetry available for this molecule Molecule 93 read successfully ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 94 read successfully INFO:: SHELXL file new-horma.ins written. LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 95 read successfully b_1: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] b_2: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.999 108.999 107.555 90 90 90 READ-INS:: Spacegroup: "I 4 2 2" INFO:: chain has 4 residues Symmetry available for this molecule Molecule 96 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.999 108.999 107.555 90 90 90 READ-INS:: Spacegroup: "I 4 2 2" INFO:: chain has 4 residues Symmetry available for this molecule Molecule 97 read successfully ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... Reading coordinate file: coot-ccp4/monomer-3GP.pdb PDB file coot-ccp4/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 98 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "3GP" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/3/3GP.cif INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:52:22_2013_modification_0.pdb.gz There are 2 data in coot-ccp4/libcheck_3GP.cif Welcome to Coot INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:52:22_2013_modification_1.pdb.gz ok test02_0 (__main__.LigandTestFunctions) Set Bond thickness test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 99 read successfully DEBUG:: there were 0 types with no dictionary here 1 ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb PDB file /home/emsley/data/greg-data/test-LIG.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 100 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb PDB file /home/emsley/data/greg-data/test-LIG.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 101 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LIG" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIG.cif INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary ok test05_0 (__main__.LigandTestFunctions) Move and Refine Ligand test ... INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:52:22_2013_modification_2.pdb.gz No graphics! Can't make Map Selection dialog. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 102 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Reading coordinate file: /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 0/113 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 0/117 INFO:: fill_ghost_info Constructed 6 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain A" Ghost 1 name: "NCS found from matching Chain E onto Chain A" Ghost 2 name: "NCS found from matching Chain G onto Chain A" Ghost 3 name: "NCS found from matching Chain D onto Chain B" Ghost 4 name: "NCS found from matching Chain F onto Chain B" Ghost 5 name: "NCS found from matching Chain H onto Chain B" Molecule 108 read successfully DEBUG:: there were 0 types with no dictionary making conventional map from MTZ filename /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT Number of OBSERVED reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.134 seconds to read MTZ file INFO:: 0.102 seconds to initialize map INFO:: 0.072 seconds for FFT INFO:: 0.006 seconds for statistics Map mean: ........ -8.79008e-07 Map sigma: ....... 0.171188 Map maximum: ..... 1.34304 Map minimum: ..... -0.695441 INFO:: 0.008 seconds for contour map INFO:: 0.322 seconds in total making difference map from MTZ filename /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT Number of OBSERVED reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.077 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.07 seconds for FFT INFO:: 0.006 seconds for statistics Map mean: ........ 2.09389e-06 Map sigma: ....... 0.0333923 Map maximum: ..... 0.366077 Map minimum: ..... -0.191665 INFO:: 0.003 seconds for contour map INFO:: 0.157 seconds in total Executing ligand search... INFO:: ligand number 0 is molecule number 102 with wiggly flag: 0 Protein centre at: xyz = ( 58.29, 34.65, 30.63) Map statistics: mean: -0.0216745 st.d: 0.0886263 Map statistics: min: -0.695441, max: 0.754209 -0.659199 14 -0.586717 143 -0.514234 1331 -0.441752 5299 -0.369269 11732 -0.296787 16725 -0.224304 21484 -0.151822 46755 -0.0793394 161104 -0.00685694 614773 0.0656256 162933 0.138108 28508 0.210591 3055 0.283073 813 0.355556 334 0.428038 197 0.500521 78 0.573003 48 0.645486 25 0.717968 9 0.790451 0 INFO:: find_clusters map_rms is 0.171132 INFO:: Using density cut-off: 0.171132 (1 sigma) (mean -0.0216776 stdev: 0.0886191) INFO:: Using water to protein distance limits: 2.4 3.2 Finding clusters...done debug:: n_ligands_for_cluster() top_score 4.04309 and 4 are decent out of 12 score_and_resort_using_correlation iclust: 0 n_ligs 12 n_sol 4 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.710467 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.650554 ----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.597263 ----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.60981 ------------------ 12 solutions for cluster 0 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 4.04309 r-state: [1 correl-score 0.710467] (atom-score: 0.404309) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 4.02776 r-state: [1 correl-score 0.650554] (atom-score: 0.402776) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 3.8627 r-state: [1 correl-score 0.60981] (atom-score: 0.38627) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 3.8769 r-state: [1 correl-score 0.597263] (atom-score: 0.38769) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 2.37512 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 2.37158 r-state: [0] (atom-score: 0.237158) many-atoms-fit: 1 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 2.06071 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.95875 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 0.649721 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.619694 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.582693 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.49419 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 2 [ligand-score: #0 at-score: 4.04309 r-state: [1 correl-score 0.710467] (atom-score: 0.404309) many-atoms-fit: 1 n-atoms: 10] limit solutions: 1 of 2 [ligand-score: #0 at-score: 4.02776 r-state: [1 correl-score 0.650554] (atom-score: 0.402776) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.01651 and 4 are decent out of 12 score_and_resort_using_correlation iclust: 1 n_ligs 12 n_sol 4 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.676577 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.688904 ----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.56899 ----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.554978 ------------------ 12 solutions for cluster 1 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 1.99864 r-state: [1 correl-score 0.688904] (atom-score: 0.199864) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 2.01651 r-state: [1 correl-score 0.676577] (atom-score: 0.201651) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.91517 r-state: [1 correl-score 0.56899] (atom-score: 0.191517) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.85929 r-state: [1 correl-score 0.554978] (atom-score: 0.185929) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.54282 r-state: [0] (atom-score: 0.154282) many-atoms-fit: 1 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.53711 r-state: [0] (atom-score: 0.153711) many-atoms-fit: 1 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.52571 r-state: [0] (atom-score: 0.152571) many-atoms-fit: 1 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.51104 r-state: [0] (atom-score: 0.151104) many-atoms-fit: 1 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 1.2013 r-state: [0] (atom-score: 0.12013) many-atoms-fit: 1 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 1.17002 r-state: [0] (atom-score: 0.117002) many-atoms-fit: 1 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 1.11377 r-state: [0] (atom-score: 0.111377) many-atoms-fit: 1 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 1.11225 r-state: [0] (atom-score: 0.111225) many-atoms-fit: 1 n-atoms: 10] limit solutions: 0 of 2 [ligand-score: #0 at-score: 1.99864 r-state: [1 correl-score 0.688904] (atom-score: 0.199864) many-atoms-fit: 1 n-atoms: 10] limit solutions: 1 of 2 [ligand-score: #0 at-score: 2.01651 r-state: [1 correl-score 0.676577] (atom-score: 0.201651) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.08817 and 4 are decent out of 12 score_and_resort_using_correlation iclust: 2 n_ligs 12 n_sol 4 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.61907 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.641407 ----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.630588 ----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.572928 ------------------ 12 solutions for cluster 2 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 2.0869 r-state: [1 correl-score 0.641407] (atom-score: 0.20869) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 2.04526 r-state: [1 correl-score 0.630588] (atom-score: 0.204526) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 2.08817 r-state: [1 correl-score 0.61907] (atom-score: 0.208817) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 2.01631 r-state: [1 correl-score 0.572928] (atom-score: 0.201631) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.25358 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.25343 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.19404 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.15181 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 0.734044 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.702536 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.609291 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.601228 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 3 [ligand-score: #0 at-score: 2.0869 r-state: [1 correl-score 0.641407] (atom-score: 0.20869) many-atoms-fit: 1 n-atoms: 10] limit solutions: 1 of 3 [ligand-score: #0 at-score: 2.04526 r-state: [1 correl-score 0.630588] (atom-score: 0.204526) many-atoms-fit: 1 n-atoms: 10] limit solutions: 2 of 3 [ligand-score: #0 at-score: 2.08817 r-state: [1 correl-score 0.61907] (atom-score: 0.208817) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.85941 and 3 are decent out of 12 score_and_resort_using_correlation iclust: 3 n_ligs 12 n_sol 3 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.21745 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.0817361 ----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.115202 ------------------ 12 solutions for cluster 3 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 1.85941 r-state: [1 correl-score 0.21745] (atom-score: 0.185941) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 1.76094 r-state: [1 correl-score 0.115202] (atom-score: 0.176094) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.80685 r-state: [1 correl-score 0.0817361] (atom-score: 0.180685) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.55964 r-state: [0] (atom-score: 0.155964) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.53921 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.53817 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.1206 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.11385 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 0.825835 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.817365 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.815745 r-state: [0] (atom-score: 0.0815745) many-atoms-fit: 1 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.741973 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.85941 r-state: [1 correl-score 0.21745] (atom-score: 0.185941) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.38901 and 3 are decent out of 12 score_and_resort_using_correlation iclust: 4 n_ligs 12 n_sol 3 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation -0.0447292 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.023702 ----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.213383 ------------------ 12 solutions for cluster 4 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 1.27054 r-state: [1 correl-score 0.213383] (atom-score: 0.127054) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 1.3219 r-state: [1 correl-score 0.023702] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.38901 r-state: [1 correl-score -0.0447292] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.23707 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.17936 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.15652 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.1559 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.15145 r-state: [0] (atom-score: 0.115145) many-atoms-fit: 1 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 1.0791 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 1.05142 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.951901 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.897714 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.27054 r-state: [1 correl-score 0.213383] (atom-score: 0.127054) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.62329 and 4 are decent out of 12 score_and_resort_using_correlation iclust: 5 n_ligs 12 n_sol 4 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.172844 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.182423 ----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.215354 ----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.18106 ------------------ 12 solutions for cluster 5 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 1.49289 r-state: [1 correl-score 0.215354] (atom-score: 0.149289) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 1.62089 r-state: [1 correl-score 0.182423] (atom-score: 0.162089) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.47803 r-state: [1 correl-score 0.18106] (atom-score: 0.147803) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.62329 r-state: [1 correl-score 0.172844] (atom-score: 0.162329) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.42128 r-state: [0] (atom-score: 0.142128) many-atoms-fit: 1 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.41456 r-state: [0] (atom-score: 0.141456) many-atoms-fit: 1 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.41066 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.3787 r-state: [0] (atom-score: 0.13787) many-atoms-fit: 1 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 0.97905 r-state: [0] (atom-score: 0.097905) many-atoms-fit: 1 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.855389 r-state: [0] (atom-score: 0.0855389) many-atoms-fit: 1 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.835225 r-state: [0] (atom-score: 0.0835225) many-atoms-fit: 1 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.755734 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.49289 r-state: [1 correl-score 0.215354] (atom-score: 0.149289) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.07828 and 2 are decent out of 12 score_and_resort_using_correlation iclust: 6 n_ligs 12 n_sol 2 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.185659 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.141778 ------------------ 12 solutions for cluster 6 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 2.07828 r-state: [1 correl-score 0.185659] (atom-score: 0.207828) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 2.03408 r-state: [1 correl-score 0.141778] (atom-score: 0.203408) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.68755 r-state: [0] (atom-score: 0.168755) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.63335 r-state: [0] (atom-score: 0.163335) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.61106 r-state: [0] (atom-score: 0.161106) many-atoms-fit: 1 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.61013 r-state: [0] (atom-score: 0.161013) many-atoms-fit: 1 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.59877 r-state: [0] (atom-score: 0.159877) many-atoms-fit: 1 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.53303 r-state: [0] (atom-score: 0.153303) many-atoms-fit: 1 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 0.942882 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.942428 r-state: [0] (atom-score: 0.0942428) many-atoms-fit: 1 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.909942 r-state: [0] (atom-score: 0.0909942) many-atoms-fit: 1 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.796521 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 1 [ligand-score: #0 at-score: 2.07828 r-state: [1 correl-score 0.185659] (atom-score: 0.207828) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.60922 and 2 are decent out of 12 score_and_resort_using_correlation iclust: 7 n_ligs 12 n_sol 2 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.224766 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.0535896 ------------------ 12 solutions for cluster 7 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 1.60922 r-state: [1 correl-score 0.224766] (atom-score: 0.160922) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 1.50926 r-state: [1 correl-score 0.0535896] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.39653 r-state: [0] (atom-score: 0.139653) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.35384 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.3487 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.189 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.17364 r-state: [0] (atom-score: 0.117364) many-atoms-fit: 1 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.10348 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 1.03613 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.982172 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.961542 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.867246 r-state: [0] (atom-score: 0.0867246) many-atoms-fit: 1 n-atoms: 10] limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.60922 r-state: [1 correl-score 0.224766] (atom-score: 0.160922) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.10846 and 2 are decent out of 12 score_and_resort_using_correlation iclust: 8 n_ligs 12 n_sol 2 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.159373 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.252585 ------------------ 12 solutions for cluster 8 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 1.99177 r-state: [1 correl-score 0.252585] (atom-score: 0.199177) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 2.10846 r-state: [1 correl-score 0.159373] (atom-score: 0.210846) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.47607 r-state: [0] (atom-score: 0.147607) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.41627 r-state: [0] (atom-score: 0.141627) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.40709 r-state: [0] (atom-score: 0.140709) many-atoms-fit: 1 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.27072 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.20091 r-state: [0] (atom-score: 0.120091) many-atoms-fit: 1 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.19269 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 0.921284 r-state: [0] (atom-score: 0.0921284) many-atoms-fit: 1 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.891549 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.728988 r-state: [0] (atom-score: 0.0728988) many-atoms-fit: 1 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.683474 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.99177 r-state: [1 correl-score 0.252585] (atom-score: 0.199177) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.81356 and 4 are decent out of 12 score_and_resort_using_correlation iclust: 9 n_ligs 12 n_sol 4 ----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.276934 ----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.376081 ----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.417633 ----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.279897 ------------------ 12 solutions for cluster 9 ------------- post correl 0 of 12 [ligand-score: #0 at-score: 1.74019 r-state: [1 correl-score 0.417633] (atom-score: 0.174019) many-atoms-fit: 1 n-atoms: 10] post correl 1 of 12 [ligand-score: #0 at-score: 1.77141 r-state: [1 correl-score 0.376081] (atom-score: 0.177141) many-atoms-fit: 1 n-atoms: 10] post correl 2 of 12 [ligand-score: #0 at-score: 1.73205 r-state: [1 correl-score 0.279897] (atom-score: 0.173205) many-atoms-fit: 1 n-atoms: 10] post correl 3 of 12 [ligand-score: #0 at-score: 1.81356 r-state: [1 correl-score 0.276934] (atom-score: 0.181356) many-atoms-fit: 1 n-atoms: 10] post correl 4 of 12 [ligand-score: #0 at-score: 1.2024 r-state: [0] (atom-score: 0.12024) many-atoms-fit: 1 n-atoms: 10] post correl 5 of 12 [ligand-score: #0 at-score: 1.17738 r-state: [0] (atom-score: 0.117738) many-atoms-fit: 1 n-atoms: 10] post correl 6 of 12 [ligand-score: #0 at-score: 1.06634 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 7 of 12 [ligand-score: #0 at-score: 1.06434 r-state: [0] (atom-score: 0.106434) many-atoms-fit: 1 n-atoms: 10] post correl 8 of 12 [ligand-score: #0 at-score: 0.607552 r-state: [0] (atom-score: 0.0607552) many-atoms-fit: 1 n-atoms: 10] post correl 9 of 12 [ligand-score: #0 at-score: 0.467374 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 10 of 12 [ligand-score: #0 at-score: 0.426473 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] post correl 11 of 12 [ligand-score: #0 at-score: 0.370657 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10] limit solutions: 0 of 2 [ligand-score: #0 at-score: 1.74019 r-state: [1 correl-score 0.417633] (atom-score: 0.174019) many-atoms-fit: 1 n-atoms: 10] limit solutions: 1 of 2 [ligand-score: #0 at-score: 1.77141 r-state: [1 correl-score 0.376081] (atom-score: 0.177141) many-atoms-fit: 1 n-atoms: 10] Symmetry available for this molecule Symmetry available for this molecule Fitting NPO gave these results: [112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126] ok test07_0 (__main__.LigandTestFunctions) Flip residue (around eigen vectors) ... Reading coordinate file: coot-ccp4/monomer-3GP.pdb PDB file coot-ccp4/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 127 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:52:34_2013_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. distance: 4.35071923863 INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:52:34_2013_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:52:34_2013_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:52:34_2013_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. distance d2: 8.6494937029e-08 ok test08_0 (__main__.LigandTestFunctions) Test dipole ... Reading coordinate file: /home/emsley/data/greg-data/dipole-residues.pdb PDB file /home/emsley/data/greg-data/dipole-residues.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 129 read successfully DEBUG:: there were 0 types with no dictionary info:: dipole components [-2.219999939203263, 4.440892098500626e-16, 0.0] ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 130 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 130 debug seq ACDEFGHIKLMNPQ storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 130 ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... Reading coordinate file: /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb PDB file /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 131 read successfully DEBUG:: there were 0 types with no dictionary valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.025 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.001 seconds for statistics Map mean: ........ 1.06932e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.019 seconds for contour map INFO:: 0.061 seconds in total storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 131 Cootaneering: imol 131 chain-id B resno 60 inscode at-name CA alt-conf Sequence: ?EYTVITPGARTR Confidence: 0.999999 From : HEYTVITPGARTR Chain id: 0 Offset: 53 INFO:: backup file coot-backup/_home_emsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Fri_Sep_13_04:52:37_2013_modification_0.pdb.gz bypassing ? at 0 Mutating to GLU at 1 Mutating poly_ala residue number 58 Mutating to TYR at 2 Mutating poly_ala residue number 59 Mutating to THR at 3 Mutating poly_ala residue number 60 Mutating to VAL at 4 Mutating poly_ala residue number 61 Mutating to ILE at 5 Mutating poly_ala residue number 62 Mutating to THR at 6 Mutating poly_ala residue number 63 Mutating to PRO at 7 Mutating poly_ala residue number 64 Mutating to GLY at 8 Mutating poly_ala residue number 65 Mutating to ALA at 9 Mutating poly_ala residue number 66 Mutating to ARG at 10 Mutating poly_ala residue number 67 Mutating to THR at 11 Mutating poly_ala residue number 68 Mutating to ARG at 12 Mutating poly_ala residue number 69 DEBUG:: Creating a new chain B WARNING:: no rotamers probabilities for residue type GLY INFO:: replace_coords: 9 atoms updated. oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: replace_coords: 12 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 8 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 7 atoms updated. WARNING:: no rotamers probabilities for residue type GLY WARNING:: no rotamers probabilities for residue type ALA INFO:: replace_coords: 11 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 11 atoms updated. ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:52:37_2013_modification_0.pdb.gz !! Warning:: No symmetry available for this molecule No Symmetry for this model There are 8 residues in chain A There are 8 residues in chain B !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: Matching/moving molecule number 135 to 135 INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 2.43677e-06 rms devi: 2.58353e-06 max devi: 4.07711e-06 min devi: 4.07e-07 INFO:: Axis orientation: ( 0.2343, -0.7118, 0.6621) INFO:: Rotation in CCP4 Polar Angles: Polar = ( 0, 0, 0) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Fri_Sep_13_04:52:38_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 1, 2.055e-08, 2.21e-08| |-2.055e-08, 1, 7.271e-09| | -2.21e-08,-7.271e-09, 1| ( -23.98, -23.98, -23.98) No unit cell for this molecule, hence no fractional matrix. ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... Reading coordinate file: /home/emsley/data/greg-data/1wly.pdb PDB file /home/emsley/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 136 read successfully DEBUG:: there were 0 types with no dictionary Reading coordinate file: /home/emsley/data/greg-data/1yb5.pdb PDB file /home/emsley/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 324/324 INFO:: NCS chain comparison 0/324 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 137 read successfully DEBUG:: there were 2 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "CL" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CL.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAP" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAP.cif INFO:: reference 136 has 750 atoms selected INFO:: moving 137 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance A 6 A 7 A 8 <---> A 2 : 0.751 A A 9 <---> A 3 : 0.942174 A A 10 <---> A 4 : 0.629981 A A 11 <---> A 5 : 0.711865 A A 12 <---> A 6 : 0.631005 A A 13 <---> A 7 : 0.467533 A A 14 <---> A 8 : 0.426381 A A 15 <---> A 9 : 0.97919 A A 16 <---> A 10 : 0.754876 A A 17 <---> A 11 : 0.488388 A A 18 <---> A 12 : 0.745058 A A 19 <---> A 13 : 0.460612 A A 20 <---> A 14 : 1.2809 A A 21 <---> A 15 : 1.24119 A A 22 <---> A 16 : 1.07334 A A 23 <---> A 17 : 0.973042 A A 24 <---> A 18 : 0.470509 A A 25 <---> A 19 : 0.355977 A A 26 <---> A 20 : 3.11453 A A 27 A 28 <---> A 21 : 1.57537 A A 29 <---> A 22 : 1.63223 A A 30 A 31 <---> A 23 : 1.9973 A A 32 <---> A 25 : 1.83236 A A 33 <---> A 26 : 0.930954 A A 34 <---> A 27 : 0.680752 A A 35 <---> A 28 : 0.267434 A A 36 <---> A 29 : 0.599491 A A 37 <---> A 30 : 0.699234 A A 38 <---> A 31 : 0.862022 A A 39 <---> A 32 : 0.842095 A A 40 <---> A 33 : 0.720834 A A 41 <---> A 34 : 0.86807 A A 42 <---> A 35 : 0.778132 A A 43 <---> A 36 : 0.621112 A A 44 <---> A 37 : 0.465701 A A 45 <---> A 38 : 0.747499 A A 46 <---> A 39 : 0.517002 A A 47 <---> A 40 : 0.505788 A A 48 <---> A 41 : 0.889736 A A 49 <---> A 42 : 0.583476 A A 50 <---> A 43 : 0.434661 A A 51 <---> A 44 : 0.619207 A A 52 <---> A 45 : 0.215003 A A 53 <---> A 46 : 0.747368 A A 54 <---> A 47 : 1.02135 A A 55 <---> A 48 : 0.920754 A A 56 <---> A 49 : 0.939245 A A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 0.466577 A A 66 <---> A 61 : 0.0522595 A A 67 <---> A 62 : 1.07191 A A 68 <---> A 63 : 0.793315 A A 69 <---> A 64 : 0.891607 A A 70 <---> A 65 : 1.25797 A A 71 <---> A 66 : 0.693217 A A 72 <---> A 67 : 1.03452 A A 73 <---> A 68 : 1.44168 A A 74 <---> A 69 : 0.909171 A A 75 <---> A 70 : 1.61656 A A 76 <---> A 71 : 0.87415 A A 77 <---> A 72 : 0.238771 A A 78 <---> A 73 : 0.311753 A A 79 <---> A 74 : 0.388701 A A 80 <---> A 75 : 0.761327 A A 81 <---> A 76 : 0.904406 A A 82 <---> A 77 : 0.609012 A A 83 <---> A 78 : 1.79778 A A 84 <---> A 79 : 1.92564 A A 85 <---> A 80 : 1.34157 A A 86 <---> A 81 : 0.565753 A A 87 <---> A 82 : 0.448017 A A 88 <---> A 83 : 0.90782 A A 89 <---> A 84 : 0.362515 A A 90 <---> A 85 : 0.404031 A A 91 <---> A 86 : 0.458593 A A 92 <---> A 87 : 0.434035 A A 93 <---> A 88 : 0.366361 A A 94 <---> A 89 : 0.492061 A A 95 <---> A 90 : 0.649822 A A 96 <---> A 91 : 1.58048 A A 97 <---> A 92 : 2.88385 A A 98 A 99 A 100 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI INFO:: backup file coot-backup/_home_emsley_data_greg-data_1yb5.pdb_Fri_Sep_13_04:52:39_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.9117, -0.3803, 0.1557| | -0.3625, 0.9227, 0.131| | -0.1935, 0.06299, -0.9791| ( 70.65, 7.793, 21.29) Rotation - polar (omega,phi,kappa) 87.1413 101.022 169.739 Rotation - euler (alpha,beta,gamma) 40.0716 168.257 18.0277 Translation - Angstroms 70.6538 7.793 21.2852 INFO: core rmsd achieved: 1.01989 Angstroems number of residues in reference structure: 322 number of residues in moving structure: 324 number of residues in aligned sections (reference): 100 number of residues in aligned sections (moving): 110 number of aligned residues: 95 number of gaps: 4 number of misdirections: 0 number of SSE combinations: 4 sequence identity: 30.5263% ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... Error reading /home/emsley/data/greg-data/1pyd.pdb 0 /home/emsley/data/greg-data/tutorial-modern.pdb 1 /home/emsley/data/greg-data/ins-code-fragment-pre.pdb 2 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 3 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 4 /home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT 5 test-3hfl.map 6 /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb 7 regression-test-terminal-residue.pdb 8 atom selection from regression-test-terminal-residue.pdb 9 /home/emsley/data/greg-data/frag-2wot.pdb 10 sphere selection from tutorial-modern.pdb 11 /home/emsley/data/greg-data/tutorial-modern.pdb 13 /home/emsley/data/greg-data/rotamer-test-fragment.pdb 14 /home/emsley/data/greg-data/res098.pdb 15 /home/emsley/data/greg-data/tutorial-modern.pdb 16 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 17 /home/emsley/data/greg-data/pdb3knw.ent 20 /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb 21 /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb 22 /home/emsley/data/greg-data/tutorial-modern.pdb 23 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 24 /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb 25 /home/emsley/data/greg-data/tutorial-modern.pdb 26 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 27 /home/emsley/data/greg-data/alt-conf-waters.pdb 28 /home/emsley/data/greg-data/backrub-fragment.pdb 29 Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb 30 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT 31 /home/emsley/data/greg-data/test-TER-OXT.pdb 32 /home/emsley/data/greg-data/val.pdb 33 /home/emsley/data/greg-data/2yie-frag.pdb 34 /home/emsley/data/greg-data/4f8g.pdb 35 /home/emsley/data/greg-data/4f8g.pdb 36 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 37 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 38 /home/emsley/data/greg-data/tutorial-modern.pdb 39 Generic Masked Map 40 difference-map 41 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 42 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 43 averaged-map 44 difference-map 45 /home/emsley/data/greg-data/multi-carbo-coot-2.pdb 46 /home/emsley/data/greg-data/monomer-VAL.pdb 47 /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb 48 atom selection from tutorial-modern.pdb 49 /home/emsley/data/greg-data/monomer-ACT.pdb 50 /home/emsley/data/greg-data/tutorial-modern.pdb 51 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 52 atom selection from tutorial-modern.pdb 53 /home/emsley/data/greg-data/tutorial-modern.pdb 54 /home/emsley/data/greg-data/tutorial-modern.pdb 55 /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb 56 /home/emsley/data/greg-data/tutorial-modern.pdb 57 /home/emsley/data/greg-data/tutorial-modern.pdb 58 /home/emsley/data/greg-data/pdb3hfl.ent 59 /home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT 60 Ideal-A-form-RNA 61 Ideal-A-form-RNA 62 Ideal-A-form-DNA 63 Ideal-A-form-DNA 64 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 65 /home/emsley/data/greg-data/some-waters-with-ter.pdb 66 /home/emsley/data/greg-data/tm+some-waters.pdb 67 /home/emsley/data/greg-data/tutorial-modern.pdb 68 /home/emsley/data/greg-data/water-test-no-cell.pdb 69 /home/emsley/data/greg-data/pathological-water-test.pdb 70 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 71 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 72 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 73 /home/emsley/data/greg-data/tutorial-modern.pdb 74 /home/emsley/data/greg-data/pdb1hvv.ent 75 /home/emsley/data/greg-data/monomer-ACT.pdb 76 /home/emsley/data/greg-data/monomer-NPO.pdb 77 SymOp_-X,-X+Y,-Z+1/3_Copy_of_74 78 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 79 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 80 /home/emsley/data/greg-data/tutorial-modern.pdb 81 /home/emsley/data/greg-data/pdb1py3.ent 82 /home/emsley/data/greg-data/tutorial-modern.pdb 83 /home/emsley/data/greg-data/tutorial-modern.pdb 84 /home/emsley/data/greg-data/2goz-manip.pdb 85 rnase_zip_test.pdb.gz 86 /home/emsley/data/greg-data/HOF.RES 87 /home/emsley/data/greg-data/hollander.ins 90 /home/emsley/data/greg-data/insulin.fcf 91 atom selection from insulin.res 92 atom selection from insulin.res 94 /home/emsley/data/greg-data/horma-p21.res 95 new-horma.ins 96 /home/emsley/data/greg-data/crash.hat 97 /home/emsley/data/greg-data/crash.hat 98 coot-ccp4/monomer-3GP.pdb 99 /home/emsley/data/greg-data/monomer-3GP.pdb 100 /home/emsley/data/greg-data/test-LIG.pdb 101 /home/emsley/data/greg-data/test-LIG.pdb 102 /home/emsley/data/greg-data/monomer-NPO.pdb 103 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 104 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 105 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 106 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 107 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 108 /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb 109 /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT 110 /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT 111 Masked (by protein) 112 Fitted ligand #0-0 113 Fitted ligand #0-1 114 Fitted ligand #1-0 115 Fitted ligand #1-1 116 Fitted ligand #2-0 117 Fitted ligand #2-1 118 Fitted ligand #2-2 119 Fitted ligand #3-0 120 Fitted ligand #4-0 121 Fitted ligand #5-0 122 Fitted ligand #6-0 123 Fitted ligand #7-0 124 Fitted ligand #8-0 125 Fitted ligand #9-0 126 Fitted ligand #9-1 127 coot-ccp4/monomer-3GP.pdb 128 Copy_of_coot-ccp4/monomer-3GP.pdb 129 /home/emsley/data/greg-data/dipole-residues.pdb 130 /home/emsley/data/greg-data/tutorial-modern.pdb 131 /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb 132 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 133 Ideal-A-form-RNA 134 Copy_of_Ideal-A-form-RNA 135 Copy_of_Ideal-A-form-RNA 136 /home/emsley/data/greg-data/1wly.pdb 137 /home/emsley/data/greg-data/1yb5.pdb ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... Reading coordinate file: /home/emsley/data/greg-data/2qd9.pdb PDB file /home/emsley/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 138 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LGF" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LGF.cif Reading coordinate file: /home/emsley/data/greg-data/2gtn.pdb PDB file /home/emsley/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 0/337 Molecule 139 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LIE" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIE.cif INFO:: reference 138 has 169 atoms selected INFO:: moving 139 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance A 140 <---> A 140 : 0.180421 A A 141 <---> A 141 : 0.0760176 A A 142 <---> A 142 : 0.105242 A A 143 <---> A 143 : 0.124554 A A 144 <---> A 144 : 0.136965 A A 145 <---> A 145 : 0.138022 A A 146 <---> A 146 : 0.166154 A A 147 <---> A 147 : 0.274391 A A 148 <---> A 148 : 0.272752 A A 149 <---> A 149 : 0.117299 A A 150 <---> A 150 : 0.168421 A A 151 <---> A 151 : 0.0928138 A A 152 <---> A 152 : 0.120023 A A 153 <---> A 153 : 0.128061 A A 154 <---> A 154 : 0.253908 A A 155 <---> A 155 : 0.635071 A A 156 <---> A 156 : 0.130036 A A 157 <---> A 157 : 0.147806 A A 158 <---> A 158 : 0.223824 A A 159 <---> A 159 : 0.227128 A A 160 <---> A 160 : 0.23718 A Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_home_emsley_data_greg-data_2gtn.pdb_Fri_Sep_13_04:52:41_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.804 -94.6984 1.24908 Rotation - euler (alpha,beta,gamma) 175.02 1.11487 -175.583 Translation - Angstroms 0.320703 0.659802 0.881869 INFO: core rmsd achieved: 0.221041 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1 sequence identity: 100% ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.025 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.001 seconds for statistics Map mean: ........ 1.06932e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.017 seconds for contour map INFO:: 0.059 seconds in total INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (45.1351,12.7252,8.80194) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7262,16.2201,23.0476) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.340548 rms devi: 0.418598 max devi: 1.61623 min devi: 0.0531786 find_ncs_matrix returns (LSQ) | 0.9705, -0.04716, -0.2363| | 0.2357, 0.3892, 0.8905| | 0.04999, -0.9199, 0.3889| ( 37.8, -17.16, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: installing ghost map with name :Map 2 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9705, -0.04716, -0.2363| | 0.2357, 0.3892, 0.8905| | 0.04999, -0.9199, 0.3889| ( 37.8, -17.16, 13.82) inverse of reference matcher transformation: | 0.9705, 0.2357, 0.04999| | -0.04716, 0.3892, -0.9199| | -0.2363, 0.8905, 0.3889| ( -33.33, 21.18, 18.84) boxing over uvw = ( 0.5483, -0.1767, -0.2832) to uvw = ( 1.229, 0.3338, 0.7954) INFO:: There were 2 maps contributing to the average INFO:: rescaling by 0.5 INFO:: 722160 out of 737280 (97.9492%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.000119555 st.d: 0.271661 Map statistics: min: -0.91788, max: 2.92726 -0.821751 70 -0.629494 2394 -0.437237 36778 -0.24498 175599 -0.0527226 280641 0.139535 130728 0.331792 56089 0.524049 28531 0.716306 14315 0.908563 6963 1.10082 3199 1.29308 1331 1.48533 464 1.67759 114 1.86985 36 2.06211 7 2.25436 10 2.44662 2 2.63888 4 2.83113 5 3.02339 0 INFO:: installing ghost map with name :Map 140 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9705, -0.04716, -0.2363| | 0.2357, 0.3892, 0.8905| | 0.04999, -0.9199, 0.3889| ( 37.8, -17.16, 13.82) inverse of reference matcher transformation: | 0.9705, 0.2357, 0.04999| | -0.04716, 0.3892, -0.9199| | -0.2363, 0.8905, 0.3889| ( -33.33, 21.18, 18.84) boxing over uvw = ( 0.5483, -0.1767, -0.2832) to uvw = ( 1.229, 0.3338, 0.7954) INFO:: There were 2 maps contributing to the average INFO:: rescaling by 0.5 INFO:: 223968 out of 228096 (98.1902%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.000217114 st.d: 0.270832 Map statistics: min: -0.915488, max: 2.77105 -0.823325 18 -0.638998 573 -0.454672 8708 -0.270345 45311 -0.0860182 84497 0.0983085 48295 0.282635 19910 0.466962 10603 0.651289 5272 0.835615 2704 1.01994 1304 1.20427 590 1.3886 198 1.57292 82 1.75725 21 1.94158 0 2.1259 4 2.31023 2 2.49456 2 2.67888 1 2.86321 1 ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... NCS info: [['A', 'B']] ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.726 77.726 77.726 90 90 90 READ-INS:: Spacegroup: "I 21 3" INFO:: chain has 121 residues Symmetry available for this molecule Molecule 145 read successfully no diffs NCS target chain has 93 peers. ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 146 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:52:43_2013_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:52:43_2013_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:52:43_2013_modification_2.pdb.gz %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.183,22.264,18.93) B-factor: 21.71 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.364276 rms devi: 0.457135 max devi: 2.1351 min devi: 0.0880999 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:52:43_2013_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:52:43_2013_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:52:43_2013_modification_5.pdb.gz ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... Reading coordinate file: /home/emsley/data/greg-data/pdb1t6q.ent PDB file /home/emsley/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 147 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Fri_Sep_13_04:52:44_2013_modification_0.pdb.gz %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.795,49.973,50.866) B-factor: 68.18 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.362,34.24,30.671) B-factor: 84.36 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.20482 rms devi: 0.265098 max devi: 1.17072 min devi: 0.0159991 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.795,49.973,50.866) B-factor: 68.18 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.664,58.992,25.996) B-factor: 67.72 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.227456 rms devi: 0.303489 max devi: 1.65495 min devi: 0.0660944 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Fri_Sep_13_04:52:44_2013_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Fri_Sep_13_04:52:44_2013_modification_2.pdb.gz result: [True, True] ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 148 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 148 and chain_id: B %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 1 Checking chains for NCS matching to chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 First atom of 540 in second selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.49888 rms devi: 2.79624 max devi: 6.68599 min devi: 0.440067 find_ncs_matrix returns (LSQ) | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) Adding ghost with name: NCS found from matching Chain A onto Chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.6728 rms devi: 2.9369 max devi: 6.12 min devi: 0.248273 find_ncs_matrix returns (LSQ) | -0.3504, -0.8022, -0.4834| | -0.7587, -0.05952, 0.6488| | -0.5492, 0.594, -0.5878| ( -29.05, 14.61, -72.53) Adding ghost with name: NCS found from matching Chain C onto Chain B INFO:: NCS chain comparison 61/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 1.73174 rms devi: 1.9769 max devi: 7.94534 min devi: 0.52974 find_ncs_matrix returns (LSQ) | -0.3815, -0.9208, -0.08098| | -0.9191, 0.3685, 0.1396| | -0.09874, 0.1277, -0.9869| ( -11.18, 4.757, -127.2) Adding ghost with name: NCS found from matching Chain D onto Chain B INFO:: NCS chain comparison 0/62 INFO:: set_ncs_master_chain Constructed 3 ghosts Ghost info:: NCS found from matching Chain A onto Chain B Ghost info:: NCS found from matching Chain C onto Chain B Ghost info:: NCS found from matching Chain D onto Chain B Symmetry available for this molecule INFO:: Matching/moving molecule number 149 to 148 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.223919 rms devi: 0.23495 max devi: 0.3369 min devi: 0.0588188 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:52:47_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) INFO:: Matching/moving molecule number 149 to 148 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.194298 rms devi: 0.211186 max devi: 0.358313 min devi: 0.0328719 INFO:: Axis orientation: ( 0.1978, -0.3281, 0.9237) INFO:: Rotation in CCP4 Polar Angles: Polar = (22.5246,-58.9204,174.877) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:52:47_2013_modification_1.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.9179, -0.212, 0.3353| | -0.04702, -0.7812, -0.6226| | 0.3939, -0.5873, 0.7071| ( 57.6, -116.4, -53.95) INFO:: fractional coordinates matrix: | -0.9451, -0.1016, -0.03159| | -0.05429, -0.754, -0.9411| | 0.3009, -0.5389, 0.7071| ( -0.109, -1.522, -0.4666) INFO:: Matching/moving molecule number 149 to 148 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.417399 rms devi: 0.453088 max devi: 0.792632 min devi: 0.0759332 INFO:: Axis orientation: ( 0.7055, 0.6938, 0.1447) INFO:: Rotation in CCP4 Polar Angles: Polar = (98.3189,-135.478,101.097) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:52:47_2013_modification_2.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.401, 0.7256, -0.5591| | 0.4417, 0.3815, 0.812| | 0.8025, -0.5726, -0.1675| ( 8.426, 15.74, -123.4) INFO:: fractional coordinates matrix: | 0.656, 0.4912, -0.1182| | 0.51, 0.1265, 1.227| | 0.6131, -0.6853, -0.1675| ( 0.1983, 0.2058, -1.067) NCS ghost chain IDs pre: [['B', 'A', 'C', 'D']] NCS ghost chain IDs post: [['B', 'A', 'C', 'D']] ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 150 read successfully DEBUG:: there were 0 types with no dictionary valid_labels(/home/emsley/data/greg-data/1hvv_sigmaa.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1 INFO:: making map from mtz filename /home/emsley/data/greg-data/1hvv_sigmaa.mtz Number of OBSERVED reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.038 seconds to read MTZ file INFO:: 0.023 seconds to initialize map INFO:: 0.026 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ -1.58391e-06 Map sigma: ....... 0.224074 Map maximum: ..... 1.72187 Map minimum: ..... -0.881789 INFO:: 0.009 seconds for contour map INFO:: 0.098 seconds in total INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.49888 rms devi: 2.79624 max devi: 6.68599 min devi: 0.440067 find_ncs_matrix returns (LSQ) | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) INFO:: NCS chain comparison 66/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.97132 rms devi: 2.1729 max devi: 4.54109 min devi: 0.429522 find_ncs_matrix returns (LSQ) | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) INFO:: NCS chain comparison 61/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.70416 rms devi: 4.0859 max devi: 9.43828 min devi: 0.285802 find_ncs_matrix returns (LSQ) | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" INFO:: installing ghost map with name :Map 151 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 151 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 151 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4 maps contributing to the average INFO:: rescaling by 0.25 INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.000831257 st.d: 0.176659 Map statistics: min: -0.997714, max: 1.48656 -0.935607 4 -0.811393 18 -0.687179 139 -0.562965 686 -0.438751 3580 -0.314537 13684 -0.190323 43824 -0.0661091 105065 0.0581048 85978 0.182319 35332 0.306533 15214 0.430747 6068 0.554961 2422 0.679174 947 0.803388 405 0.927602 206 1.05182 85 1.17603 38 1.30024 9 1.42446 8 1.54867 0 INFO:: installing ghost map with name :Map 151 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 151 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 151 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4 maps contributing to the average INFO:: rescaling by 0.25 INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.000831257 st.d: 0.176659 Map statistics: min: -0.997714, max: 1.48656 -0.935607 4 -0.811393 18 -0.687179 139 -0.562965 686 -0.438751 3580 -0.314537 13684 -0.190323 43824 -0.0661091 105065 0.0581048 85978 0.182319 35332 0.306533 15214 0.430747 6068 0.554961 2422 0.679174 947 0.803388 405 0.927602 206 1.05182 85 1.17603 38 1.30024 9 1.42446 8 1.54867 0 INFO:: installing ghost map with name :Map 151 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 151 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 151 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4 maps contributing to the average INFO:: rescaling by 0.25 INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.000831257 st.d: 0.176659 Map statistics: min: -0.997714, max: 1.48656 -0.935607 4 -0.811393 18 -0.687179 139 -0.562965 686 -0.438751 3580 -0.314537 13684 -0.190323 43824 -0.0661091 105065 0.0581048 85978 0.182319 35332 0.306533 15214 0.430747 6068 0.554961 2422 0.679174 947 0.803388 405 0.927602 206 1.05182 85 1.17603 38 1.30024 9 1.42446 8 1.54867 0 BL DEBUG:: molecule_names ['/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/ins-code-fragment-pre.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'test-3hfl.map', '/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb', 'regression-test-terminal-residue.pdb', 'atom selection from regression-test-terminal-residue.pdb', '/home/emsley/data/greg-data/frag-2wot.pdb', 'sphere selection from tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rotamer-test-fragment.pdb', '/home/emsley/data/greg-data/res098.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/pdb3knw.ent', '/home/emsley/data/greg-data/alt-conf-pepflip-test.pdb', '/home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/alt-conf-waters.pdb', '/home/emsley/data/greg-data/backrub-fragment.pdb', 'Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT', '/home/emsley/data/greg-data/test-TER-OXT.pdb', '/home/emsley/data/greg-data/val.pdb', '/home/emsley/data/greg-data/2yie-frag.pdb', '/home/emsley/data/greg-data/4f8g.pdb', '/home/emsley/data/greg-data/4f8g.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/tutorial-modern.pdb', 'Generic Masked Map', 'difference-map', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'averaged-map', 'difference-map', '/home/emsley/data/greg-data/multi-carbo-coot-2.pdb', '/home/emsley/data/greg-data/monomer-VAL.pdb', '/home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb', 'atom selection from tutorial-modern.pdb', '/home/emsley/data/greg-data/monomer-ACT.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', 'atom selection from tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb3hfl.ent', '/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Ideal-A-form-RNA', 'Ideal-A-form-RNA', 'Ideal-A-form-DNA', 'Ideal-A-form-DNA', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/some-waters-with-ter.pdb', '/home/emsley/data/greg-data/tm+some-waters.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/water-test-no-cell.pdb', '/home/emsley/data/greg-data/pathological-water-test.pdb', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb1hvv.ent', '/home/emsley/data/greg-data/monomer-ACT.pdb', '/home/emsley/data/greg-data/monomer-NPO.pdb', 'SymOp_-X,-X+Y,-Z+1/3_Copy_of_74', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb1py3.ent', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/2goz-manip.pdb', 'rnase_zip_test.pdb.gz', '/home/emsley/data/greg-data/HOF.RES', '/home/emsley/data/greg-data/hollander.ins', '/home/emsley/data/greg-data/insulin.fcf', 'atom selection from insulin.res', 'atom selection from insulin.res', '/home/emsley/data/greg-data/horma-p21.res', 'new-horma.ins', '/home/emsley/data/greg-data/crash.hat', '/home/emsley/data/greg-data/crash.hat', 'coot-ccp4/monomer-3GP.pdb', '/home/emsley/data/greg-data/monomer-3GP.pdb', '/home/emsley/data/greg-data/test-LIG.pdb', '/home/emsley/data/greg-data/test-LIG.pdb', '/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', '/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb', '/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT', '/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT', 'Masked (by protein)', 'Fitted ligand #0-0', 'Fitted ligand #0-1', 'Fitted ligand #1-0', 'Fitted ligand #1-1', 'Fitted ligand #2-0', 'Fitted ligand #2-1', 'Fitted ligand #2-2', 'Fitted ligand #3-0', 'Fitted ligand #4-0', 'Fitted ligand #5-0', 'Fitted ligand #6-0', 'Fitted ligand #7-0', 'Fitted ligand #8-0', 'Fitted ligand #9-0', 'Fitted ligand #9-1', 'coot-ccp4/monomer-3GP.pdb', 'Copy_of_coot-ccp4/monomer-3GP.pdb', '/home/emsley/data/greg-data/dipole-residues.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', '/home/emsley/data/greg-data/1wly.pdb', '/home/emsley/data/greg-data/1yb5.pdb', '/home/emsley/data/greg-data/2qd9.pdb', '/home/emsley/data/greg-data/2gtn.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Map 2 NCS average of Chain A type molecules', 'Map 140 NCS average of Chain A type molecules', '/home/emsley/data/greg-data/insulin.res', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb1t6q.ent', '/home/emsley/data/greg-data/pdb1hvv.ent', '/home/emsley/data/greg-data/pdb1hvv.ent', '/home/emsley/data/greg-data/1hvv_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Map 151 NCS found from matching Chain B onto Chain A', 'Map 151 NCS found from matching Chain C onto Chain A', 'Map 151 NCS found from matching Chain D onto Chain A', 'Map 151 NCS average of Chain A type molecules', 'Map 151 NCS found from matching Chain B onto Chain A', 'Map 151 NCS found from matching Chain C onto Chain A', 'Map 151 NCS found from matching Chain D onto Chain A', 'Map 151 NCS average of Chain A type molecules'] BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... INFO:: key missing not found in code table ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... BL DEBUG:: return scheme is [24.219083786010742, -41.04264831542969, -67.95923614501953] ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... Entering test: kevin's torsion test PASS: kevin's torsion test Entering test: test_alt_conf_rotamers Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_alt_conf_rotamers Entering test: test_wiggly_ligands There are 2 data in /home/emsley/data/greg-data/libcheck_BUA.cif get_monomer type: BUA This residues has 2 defined non-H torsions of which 2 are (non-const) rotatable and 2 are non-const and non-ring torsions PASS: test_wiggly_ligands Entering test: test_fragmemt_atom_selection Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 n_initial: 1465 n_1: 1401 n_2: 64 PASS: test_fragmemt_atom_selection Entering test: test_add_atom Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_add_atom Entering test: test dictionary partial charges INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif There are 1 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif PASS: test dictionary partial charges Entering test: test segid exchange Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Test with a rogue segid INFO:: No consistent segids for residue 1 PASS: test segid exchange Entering test: test ligand from point There are 2 data in /home/emsley/data/greg-data/libcheck_3GP-torsion-filtered.cif Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... get_monomer type: 3GP This residues has 16 defined non-H torsions of which 4 are (non-const) rotatable and 4 are non-const and non-ring torsions 0 [torsion-restraint: CONST_var_4 C1* O4* C4* C5* 124.212 20 1 CONST ] 1 [torsion-restraint: var_13 C3* O3* P O2P -156.991 20 1] 2 [torsion-restraint: var_2 C8 N9 C1* C2* -78.375 20 1] 3 [torsion-restraint: CONST_8 C5 N7 C8 N9 0 0 0 CONST ] 4 [torsion-restraint: CONST_5 C4 N3 C2 N1 0 0 0 CONST ] 5 [torsion-restraint: CONST_9 N7 C8 N9 C1* 180 0 0 CONST ] 6 [torsion-restraint: CONST_1 O6 C6 C5 N7 0 0 0 CONST ] 7 [torsion-restraint: CONST_7 C6 C5 N7 C8 180 0 0 CONST ] 8 [torsion-restraint: CONST_2 C6 C5 C4 N3 0 0 0 CONST ] 9 [torsion-restraint: var_6 O4* C4* C5* O5* -61.686 20 3] 10 [torsion-restraint: CONST_4 C5 C4 N3 C2 0 0 0 CONST ] 11 [torsion-restraint: var_12 C2* C3* O3* P -179.703 20 1] 12 [torsion-restraint: CONST_var_10 C1* C2* C3* O3* 82.074 20 3 CONST ] 13 [torsion-restraint: CONST_6 N3 C2 N1 C6 0 0 0 CONST ] 14 [torsion-restraint: CONST_var_3 N9 C1* O4* C4* -152.904 20 1 CONST ] 15 [torsion-restraint: CONST_var_8 N9 C1* C2* C3* 155.484 20 3 CONST ] created 38 bond restraints created 66 angle restraints created 1 plane restraints created 4 chiral vol restraints created 109 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 29.8478 Initial RMS Z values bonds: 0.123586 angles: 0.421281 torsions: N/A planes: 0.0585508 non-bonded: 0.0231537 chiral vol: N/A rama plot: N/A start_pos: N/A INFO:: setup minimol from mol: no spacegroup ligand eigen values: 20.3246 94.025 434.445 ligand eigen vectors: | -0.14, 0.1847, -0.9728| | -0.1574, 0.9658, 0.206| | 0.9776, 0.182, -0.1061| created 38 bond restraints created 66 angle restraints created 1 plane restraints created 4 chiral vol restraints created 109 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 12.2973 Initial RMS Z values bonds: 0.123584 angles: 0.421281 torsions: N/A planes: 0.0585508 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A INFO:: setup minimol from mol: no spacegroup ligand eigen values: 28.8334 89.8786 427.176 ligand eigen vectors: | -0.1106, 0.2223, -0.9687| | -0.2631, 0.9333, 0.2443| | 0.9584, 0.2819, -0.04476| created 38 bond restraints created 66 angle restraints created 1 plane restraints created 4 chiral vol restraints created 109 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 1953.91 Initial RMS Z values bonds: 0.123584 angles: 0.421281 torsions: N/A planes: 0.0585508 non-bonded: 2.52814 chiral vol: N/A rama plot: N/A start_pos: N/A INFO:: setup minimol from mol: no spacegroup ligand eigen values: 26.987 97.7834 417.459 ligand eigen vectors: | -0.06051, 0.2019, -0.9775| | -0.2629, 0.9415, 0.2108| | 0.9629, 0.2698, -0.003868| created 38 bond restraints created 66 angle restraints created 1 plane restraints created 4 chiral vol restraints created 109 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 12.2974 Initial RMS Z values bonds: 0.123585 angles: 0.421281 torsions: N/A planes: 0.0585508 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A INFO:: setup minimol from mol: no spacegroup ligand eigen values: 19.953 97.5201 427.055 ligand eigen vectors: | -0.1658, 0.1643, -0.9724| | -0.1516, 0.97, 0.1898| | 0.9744, 0.1789, -0.1359| created 38 bond restraints created 66 angle restraints created 1 plane restraints created 4 chiral vol restraints created 109 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links initial distortion_score: 12.2973 Initial RMS Z values bonds: 0.123585 angles: 0.421281 torsions: N/A planes: 0.0585508 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A Minimum found (iteration number 851) at 8.75477 Final Estimated RMS Z Scores: bonds: 0.102213 angles: 0.355855 torsions: N/A planes: 0.000798656 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A INFO:: setup minimol from mol: no spacegroup ligand eigen values: 44.3487 72.939 441.358 ligand eigen vectors: | -0.08365, 0.2384, -0.9676| | -0.524, 0.8154, 0.2462| | 0.8476, 0.5276, 0.05671| Protein centre at: xyz = ( 41.53, 8.726, 12.87) There are 1 clusers Here are the top 10 clusers: Number: 0 # grid points: 264 score: 146.595 | -0.1765, 0.981, -0.08001| | 0.2847, 0.1287, 0.9499| | 0.9422, 0.1449, -0.302| ( 55.49, 9.316, 20.62) xyz = ( 3.05, 1.281, 0.8881) eigenvalues: 131.008 2545.35 421.94 found distance from reference centre 0.616329 PASS: test ligand from point Entering test: test peak search non-close reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... map rms: 0.311493, peak cut-off: 0.155746 INFO:: peak filtering: npeaks: in: 5158 out: 2105 There are 2105 peaks and 0 problem peaks PASS: test peak search non-close Entering test: test symop card 1 0 0 0 1 0 0 0 1 translations: -1 0 0 PASS: test symop card Entering test: test rotate round vector Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 0 O6 0.939693 -> 20 degrees 1 C6 0.939693 -> 20 degrees 2 C5 0.939693 -> 20 degrees 3 C4 0.939693 -> 20 degrees 4 N3 0.939693 -> 20 degrees 5 C2 0.939693 -> 20 degrees 6 N2 0.939693 -> 20 degrees 7 HN22 0.939693 -> 20 degrees 8 HN21 0.939693 -> 20 degrees 9 N1 0.939693 -> 20 degrees 10 HN1 0.939693 -> 20 degrees 11 N7 0.939693 -> 20 degrees 12 C8 0.939693 -> 20 degrees 13 H8 0.939693 -> 20 degrees 16 H1* 0.939693 -> 20 degrees 17 O4* 0.939693 -> 20 degrees 18 C4* 0.939693 -> 20 degrees 19 H4* 0.939693 -> 20 degrees 20 C5* 0.939693 -> 20 degrees 21 H5*1 0.939693 -> 20 degrees 22 H5*2 0.939693 -> 20 degrees 23 O5* 0.939693 -> 20 degrees 24 HO5* 0.939693 -> 20 degrees 25 C2* 0.939693 -> 20 degrees 26 H2* 0.939693 -> 20 degrees 27 O2* 0.939693 -> 20 degrees 28 HO2* 0.939693 -> 20 degrees 29 C3* 0.939693 -> 20 degrees 30 H3* 0.939693 -> 20 degrees 31 O3* 0.939693 -> 20 degrees 32 P 0.939693 -> 20 degrees 33 O1P 0.939693 -> 20 degrees 34 O3P 0.939693 -> 20 degrees 35 O2P 0.939693 -> 20 degrees PASS: test rotate round vector Entering test: SSM sequence alignment output -- Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC -- Moving: D Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG -- Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG -- PASS: SSM sequence alignment output ok ---------------------------------------------------------------------- Ran 118 tests in 448.153s OK test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... ok test07_1 (__main__.PdbMtzTestFunctions) Auto-read bad MTZ test ... ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... ok test09_1 (__main__.PdbMtzTestFunctions) Sharpen map from map ... ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... ok test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... ok test16_3 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... ok test29_1 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... ok test32_0 (__main__.PdbMtzTestFunctions) Test for mangling of hydrogen names from a PDB v 3.0 ... ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... ok test98_0 (__main__.PdbMtzTestFunctions) Hundreds of Ramachandran refinements (post_manipulation_hook_py test) ... ok test99_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... ok test02_0 (__main__.LigandTestFunctions) Set Bond thickness test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... ok test05_0 (__main__.LigandTestFunctions) Move and Refine Ligand test ... ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... ok test07_0 (__main__.LigandTestFunctions) Flip residue (around eigen vectors) ... ok test08_0 (__main__.LigandTestFunctions) Test dipole ... ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... ok test02_0 (gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "redefine-functions.scm" load "json-reader.scm" load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" load "local-code.scm" load "hello.scm" Good morning Paul Emsley. Welcome to Coot 0.8-pre (revision 4759) [with guile 1.8.8 embedded] [with python 2.7.5 embedded]. load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "parse-pisa-xml.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "prodrg-import.scm" load "jligand.scm" load "americanisms.scm" load "group-settings.scm" Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message. __main__.CootaneerTestFunctions) Cootaneer Beta Strand ... ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... ok ---------------------------------------------------------------------- Ran 118 tests in 448.153s OK Unitest skip does not exist! The following tests were skipped and marked as passed: Libcif horne FINALLY collect some GARBAGE BL INFO:: no of collected carbage items 6 BL DEBUG:: list of garbage items: (, , ) Detailed information for functions: BL INFO:: garbage item and location: BL INFO:: garbage item and location: test_coot_python: coot test passed