testing with greg testing with greg currently we are here: /home/emsley/autobuild/building/garib-pc-1.lmb.internal_2013-09-13__T03_40_01/coot-0.8-pre Fri Sep 13 04:44:04 BST 2013 WARNING:: ccp4 setup file setup-ccp4 does not exist. /home/emsley/autobuild/installed-pre-release-gtk2-python/bin/coot-real --no-graphics --script command-line-greg.scm 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. 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 Molecule number -5 is not a valid model molecule Reading coordinate file: /home/emsley/data/greg-data/2WF6.cif mmCIF file /home/emsley/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 1 read successfully DEBUG:: there were 3 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "ALF" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALF.cif INFO:: using standard CCP4 Refmac dictionary to search for "MG" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MG.cif INFO:: using standard CCP4 Refmac dictionary to search for "BG6" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/b/BG6.cif in new_molecule_by_atom_selection Something bad happened - No atoms selected 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 2 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Creating directory coot-backup INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:44:04_2013_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:44:04_2013_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:44:04_2013_modification_2.pdb.gz WARNING:: Error reading bogus.map Read map bogus.map failed 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:: 0.003 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.05 seconds for contour map INFO:: 0.152 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (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 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:: 0.034 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:: 0.047 seconds for contour map INFO:: 0.109 seconds in total 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:: 0.022 seconds to read MTZ file INFO:: 0.018 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 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 7 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_04:44:05_2013_modification_0.pdb.gz Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:05_2013_modification_0.pdb.gz 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_04:44:05_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_04:44:05_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 Symmetry available for this molecule Symmetry available for this molecule N /10/B is not found in this molecule: (11) atom selection from tutorial-modern.pdb INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:05_2013_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:05_2013_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:05_2013_modification_2.pdb.gz 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 12 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 ""] 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 13 read successfully DEBUG:: there were 0 types with no dictionary 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): 2.221 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_res098.pdb_Fri_Sep_13_04:44:06_2013_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. 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 14 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:: 0.025 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:: 0.05 seconds for contour map INFO:: 0.111 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_04:44:07_2013_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 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_04:44:07_2013_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 12.0506 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 16 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_04:44:07_2013_modification_0.pdb.gz 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" === greg-tests tests === Loading greg-tests/begin.grg ... =============================================================== ==================== Testing ================================== =============================================================== Loaded greg-tests/begin.grg Running 01-pdb+mtz.scm ... Entered testcase - Post Go To Atom no molecules PASS: Post Go To Atom no molecules Entered testcase - Close bad molecule PASS: Close bad molecule Entered testcase - Read coordinates test PASS: Read coordinates test Entered testcase - New molecule from bogus molecule PASS: New molecule from bogus molecule Entered testcase - Don't crash on empty NCS from mmCIF file closing molecule number 1 PASS: Don't crash on empty NCS from mmCIF file Entered testcase - New molecule from bogus atom selection INFO:: pre-n-molecules 2 post-n-molecules 2 PASS: New molecule from bogus atom selection Entered testcase - ins code change and Goto atom over an ins code break 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 ") PASS: ins code change and Goto atom over an ins code break Entered testcase - Read a bogus map PASS: Read a bogus map Entered testcase - Read MTZ test PASS: Read MTZ test Entered testcase - Auto-read bad MTZ test got status: -1 got status: -1 PASS: Auto-read bad MTZ test Entered testcase - Map Sigma INFO:: map sigmas 0.311500996351242 #f PASS: Map Sigma Entered testcase - Another Level Test PASS: Another Level Test Entered testcase - Sharpen map from map PASS: Sharpen map from map Entered testcase - Set Atom Attribute Test PASS: Set Atom Attribute Test Entered testcase - Add Terminal Residue Test PASS: Add Terminal Residue Test Entered testcase - Adding residue by phi psi, no crash PASS: Adding residue by phi psi, no crash Entered testcase - Select by Sphere Sphere mol: there are 4 residues in chain "B" Found 20 sphere atoms PASS: Select by Sphere Entered testcase - Test Views PASS: Test Views Entered testcase - Label Atoms and Delete PASS: Label Atoms and Delete Entered testcase - Rotamer outliers PASS: Rotamer outliers Entered testcase - Alt Conf Occ Sum Reset For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 PASS: Alt Conf Occ Sum Reset Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue PASS: Correct occupancies after auto-fit rotamer on alt-confed residue Entered testcase - Rotamers work on MSE se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746)) se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616)) PASS: Rotamers work on MSE Entered testcase - Splitting residuReading 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 17 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:: 0.002 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_04:44:07_2013_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" 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 19 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_04:44:08_2013_modification_0.pdb.gz flipped 65 A 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 20 read successfully DEBUG:: there were 0 types with no dictionary in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x3347530 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_04:44:08_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_04:44:08_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_04:44:08_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): 3.876 Refinement elapsed time: 0.016 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_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_04:44:08_2013_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.73012 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): 4.005 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_04:44:08_2013_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. 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 21 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:: 0.048 seconds for contour map INFO:: 0.108 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): 4.414 Refinement elapsed time: 0.007 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:09_2013_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. 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 23 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_04:44:09_2013_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" 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 25) at -11238.9 Final Estimated RMS Z Scores: bonds: 1.07026 angles: 0.634336 torsions: N/A planes: 0.854652 non-bonded: 0 chiral vol: 0.212403 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 4.974 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:09_2013_modification_1.pdb.gz INFO:: replace_coords: 23 atoms updated. 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 28) at -16252.4 Final Estimated RMS Z Scores: bonds: 1.61921 angles: 1.6368 torsions: N/A planes: 1.89061 non-bonded: 0.00148114 chiral vol: 2.20098 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 5.378 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:09_2013_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. 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 24 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:: 0.048 seconds for contour map INFO:: 0.108 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): 5.9 Refinement elapsed time: 0.088 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): 6.053 Refinement elapsed time: 0.152 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): 6.202 Refinement elapsed time: 0.149 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): 6.397 Refinement elapsed time: 0.194 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): 6.649 Refinement elapsed time: 0.251 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): 6.89 Refinement elapsed time: 0.241 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 26 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_04:44:11_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 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 27 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_04:44:12_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Fri_Sep_13_04:44:12_2013_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. Reading coordinate file: /home/emsley/data/greg-data/coords-B3A.pdb PDB file /home/emsley/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 29 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "B3A" There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/b/B3A.cif created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 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: 2.9511 Initial RMS Z values bonds: 0.661891 angles: 0.373663 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.249961 rama plot: N/A start_pos: N/A Minimum found (iteration number 28) at 4.05831e-05 Final Estimated RMS Z Scores: bonds: 0.000532687 angles: 0.00277865 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.00074825 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 7.766 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Fri_Sep_13_04:44:12_2013_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/lib-B3A.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/lib-B3A.cif had no bond restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 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: 4.05831e-05 Initial RMS Z values bonds: 0.000532687 angles: 0.00277865 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.00074825 rama plot: N/A start_pos: N/A Minimum found (iteration number 2) at 3.06826e-05 Final Estimated RMS Z Scores: bonds: 0.00034354 angles: 0.0024396 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.00057811 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 7.835 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Fri_Sep_13_04:44:12_2013_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. There are 3 data in /home/emsley/data/greg-data/lib-both.cif Welcome to Coot created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 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: 3.01935 Initial RMS Z values bonds: 0.670842 angles: 0.375491 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.253458 rama plot: N/A start_pos: N/A Minimum found (iteration number 30) at 3.9422e-06 Final Estimated RMS Z Scores: bonds: 0.000590566 angles: 0.000608582 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.000588644 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 7.904 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Fri_Sep_13_04:44:12_2013_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. 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:: 0.025 seconds to read MTZ file INFO:: 0 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:: 0.043 seconds for contour map INFO:: 0.103 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. 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_04:44:13_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 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_04:44:13_2013_modification_0.pdb.gz 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_04:44:13_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 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_04:44:14_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 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_04:44:14_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 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:: 0.042 seconds for contour map INFO:: 0.103 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:: 0.001 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:: 0.041 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 e leaves no atoms with negative occupancy PASS: Splitting residue leaves no atoms with negative occupancy Entered testcase - Pepflip flips the correct alt confed atoms PASS: Pepflip flips the correct alt confed atoms Entered testcase - Correction of CISPEP test CISPEPs: "3" PASS: Correction of CISPEP test Entered testcase - Refine Zone with Alt conf refined moved: d=0.29338761868981 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.29549296880026 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 1.683" 1.6828066110611) ("Angles" "Angles: 1.810" 1.81047487258911) ("Planes" "Planes: 2.091" 2.09142184257507) ("Non-bonded" "Non-bonded: 0.058" 0.0580132193863392) ("Chirals" "Chirals: 2.425" 2.4250476360321))) ow factor: 2.00243774056435 INFO:: setting refinement weight to 14.963500637066 refinement results: ("" 0 (("Bonds" "Bonds: 0.476" 0.476411163806915) ("Angles" "Angles: 1.303" 1.30327272415161) ("Planes" "Planes: 1.972" 1.97226870059967) ("Non-bonded" "Non-bonded: 0.028" 0.028261985629797) ("Chirals" "Chirals: 1.282" 1.28201711177826))) ow factor: 1.25849242508411 INFO:: setting refinement weight to 9.44782857351441 refinement results: ("" 0 (("Bonds" "Bonds: 0.349" 0.349261254072189) ("Angles" "Angles: 1.240" 1.23969268798828) ("Planes" "Planes: 1.959" 1.95912933349609) ("Non-bonded" "Non-bonded: 0.024" 0.0239320993423462) ("Chirals" "Chirals: 1.142" 1.14170038700104))) ow factor: 1.1724459156394 INFO:: setting refinement weight to 6.87300018487727 refinement results: ("" 0 (("Bonds" "Bonds: 0.299" 0.29859334230423) ("Angles" "Angles: 1.213" 1.21292293071747) ("Planes" "Planes: 1.945" 1.94519364833832) ("Non-bonded" "Non-bonded: 0.023" 0.0227481555193663) ("Chirals" "Chirals: 1.082" 1.08217918872833))) ow factor: 1.13472227752209 INFO:: setting refinement weight to 5.33786014132015 refinement results: ("" 0 (("Bonds" "Bonds: 0.272" 0.272194415330887) ("Angles" "Angles: 1.197" 1.19711756706238) ("Planes" "Planes: 1.930" 1.93037307262421) ("Non-bonded" "Non-bonded: 0.022" 0.022380568087101) ("Chirals" "Chirals: 1.046" 1.04578804969788))) ow factor: 1.11136827617884 INFO:: setting refinement weight to 4.32166596876805 refinement results: ("" 0 (("Bonds" "Bonds: 0.257" 0.256858438253403) ("Angles" "Angles: 1.186" 1.18564605712891) ("Planes" "Planes: 1.916" 1.91639447212219) ("Non-bonded" "Non-bonded: 0.022" 0.0223261024802923) ("Chirals" "Chirals: 1.020" 1.02023339271545))) ow factor: 1.09478309005499 PASS: Refinement gives useful results Entered testcase - Rigid Body Refine Alt Conf Waters PASS: Rigid Body Refine Alt Conf Waters Entered testcase - Setting multiple atom attributes PASS: Setting multiple atom attributes Entered testcase - Tweak Alt Confs on Active Residue PASS: Tweak Alt Confs on Active Residue Entered testcase - Backrub rotamer PASS: Backrub rotamer Entered testcase - Libcif horne PASS: Libcif horne Entered testcase - Refmac Parameters Storage PASS: Refmac Parameters Storage Entered testcase - OXT is added before TER record - add only one found TER "TER 25 ASP A 14 " PASS: OXT is added before TER record - add only one Entered testcase - The position of the oxygen after a mutation PASS: The position of the oxygen after a mutation Entered testcase - TER is at the end of a nucleotide after mutation PASS: TER is at the end of a nucleotide after mutation Entered testcase - C7 is removed on mutation from a DC PASS: C7 is removed on mutation from a DC Entered testcase - C7 is added on mutation to a DC DEBUG:: atoms is (" P " " OP1" " OP2" " O5'" " C5'" " C4'" " O4'" " C3'" " O3'" " C2'" " C1'" " N1 " " C2 " " N3 " " C4 " " C5 " " C6 " " O2 " " O4 " " C7 ") PASS: C7 is added on mutation to a DC Entered testcase - Mask and difference map high-values: (0.989829301834106 0.952502369880676 1.01570284366608 0.636203646659Map 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 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:: 0.028 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.035 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:: 0.048 seconds for contour map INFO:: 0.114 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:: 0.004 seconds for statistics Map mean: ........ 1.16132e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.054 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 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 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): 12.559 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_multi-carbo-coot-2.pdb_Fri_Sep_13_04:44:17_2013_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. 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): 13.196 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:17_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_04:44:17_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_04:44:17_2013_modification_0.pdb.gz PDB file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:17_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): 13.282 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:18_2013_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. 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): 14.111 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_04:44:18_2013_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. 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 63) at -272.29 Final Estimated RMS Z Scores: bonds: 0.260688 angles: 0.23195 torsions: N/A planes: 0.209858 non-bonded: 0.00234627 chiral vol: 0.0806383 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 14.177 Refinement elapsed time: 0.024 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:18_2013_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. 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: 3426.1 Initial RMS Z values bonds: 17.5578 angles: 0.23195 torsions: N/A planes: 0.209858 non-bonded: 0 chiral vol: 0.0806383 rama plot: N/A start_pos: N/A Minimum found (iteration number 31) at -313.089 Final Estimated RMS Z Scores: bonds: 0.0783225 angles: 0.100718 torsions: N/A planes: 0.267083 non-bonded: 0 chiral vol: 0.018268 rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 14.214 Refinement elapsed time: 0.024 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:18_2013_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. -- new structure created SUMMARY:: rc CIFRC_Ok or newly created. 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 WARNING:: bond_restraint_length 4 should be 5 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 13) at -79.5267 Final Estimated RMS Z Scores: bonds: 0.0186632 angles: 0.103515 torsions: N/A planes: 0.0257578 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A SUCCESS TIME:: (dragged refinement): 15 Refinement elapsed time: 0.049 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-ACT.pdb_Fri_Sep_13_04:44:19_2013_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. 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_04:44:20_2013_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_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_04:44:20_2013_modification_2.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_3.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_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_04:44:20_2013_modification_6.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_7.pdb.gz Symmetry available for this molecule Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. 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 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 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:21_2013_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint 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 INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] 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_04:44:22_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 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_04:44:23_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_04:44:24_2013_modification_0.pdb.gz 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:: 0.025 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:: 0.054 seconds in total INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Fri_Sep_13_04:44:25_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_04:44:25_2013_modification_1.pdb.gz 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_04:44:25_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:44:25_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 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_04:44:25_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:44:25_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 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_04:44:25_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 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_04:44:25_2013_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_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 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_04:44:25_2013_modification_0.pdb.gz 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_04:44:26_2013_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule 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 2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.311501 INFO:: Using density cut-off: 0.623002 (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 = ( 59.88, 3.015, -4.288) is too big to be water INFO:: cluster at xyz = ( 70.02, 19.08, 18.63) is too big to be water INFO:: cluster at xyz = ( 53, 9.031, 20.13) is too big to be water INFO:: found 62 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_04:44:27_2013_modification_0.pdb.gz INFO:: Adding to solvent chain: D 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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_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_04:44:27_2013_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule 851 0.687578678131104 0.801753640174866 0.738103628158569 1.06824910640717 1.01713156700134 1.01199650764465 0.822739899158478) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) 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: (-0.893179178237915 -0.947303891181946 -1.18386626243591 -1.29074656963348 -1.08600687980652 -0.827113330364227 -0.848896384239197 -0.693203151226044 -0.970726788043976 -0.553648889064789) PASS: Mask and difference map Entered testcase - Simple Averaged maps INFO:: map sigmas: normal 0.311048001050949 and diff-map: 0.00108590547461063 PASS: Simple Averaged maps Entered testcase - Make a glycosidic linkage bond-length: 2.97694066606539: bond-length: 1.44039386011154: PASS: Make a glycosidic linkage Entered testcase - Test for flying hydrogens on undo PASS: Test for flying hydrogens on undo Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0 PASS: Test for mangling of hydrogen names from a PDB v 3.0 Entered testcase - correct matching dictionary names from test name PASS: correct matching dictionary names from test name Entered testcase - update monomer restraints Bond-length: 2.84994989549065: pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.51394823659121: PASS: update monomer restraints Entered testcase - Write mmCIF restraints correctly PASS: Write mmCIF restraints correctly Entered testcase - Refinement OK with zero bond esd PASS: Refinement OK with zero bond esd Entered testcase - Change Chain IDs and Chain Sorting PASS: Change Chain IDs and Chain Sorting Entered testcase - Replace Fragment distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) PASS: Replace Fragment Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () PASS: Residues in Region of Residue Entered testcase - Residues in region of a point PASS: Residues in region of a point Entered testcase - Empty molecule on type selection PASS: Empty molecule on type selection Entered testcase - Set Rotamer PASS: Set Rotamer Entered testcase - Rotamer names and scores are correct Rotamer 0 : "m-85" 100.0 Rotamer 1 : "t80" 90.1668395996094 Rotamer 2 : "p90" 50.7077865600586 Rotamer 3 : "m -30 " 21.4231548309326 Rotamer 4 : "m -30 " 21.4231548309326 PASS: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions ::::: (55 "A" 1 "") #f #f ::::: (55 "A" 4 "") #t #t ::::: (55 "A" 59 "") #t #t ::::: (55 "A" 60 "") #f #f ::::: (55 "A" 61 "") #f #f ::::: (55 "A" 92 "") #t #t ::::: (55 "A" 94 "") #f #f PASS: Align and mutate a model with deletions Entered testcase - renumbered residues should be in seqnum order PASS: renumbered residues should be in seqnum order Entered testcase - Autofit Rotamer on Residues with Insertion codes PASS: Autofit Rotamer on Residues with Insertion codes Entered testcase - RNA base has correct residue type after mutation mutated base to type "C" - was "A" mutated base to type "Cr" - was "A" PASS: RNA base has correct residue type after mutation Entered testcase - DNA bases are the correct residue type after mutation mutated base to type "DC" mutated base to type "DG" mutated base to type "DA" mutated base to type "DT" mutated base to type "Cd" mutated base to type "Gd" mutated base to type "Ad" mutated base to type "Td" PASS: DNA bases are the correct residue type after mutation Entered testcase - SegIDs are correct after mutate PASS: SegIDs are correct after mutate Entered testcase - TER on water chain is removed on adding a water by hand PASS: TER on water chain is removed on adding a water by hand Entered testcase - TER on water chain is removed on adding waters automatically PASS: TER on water chain is removed on adding waters automatically Entered testcase - Adding atoms to Many-Chained Molecule PASS: Adding atoms to Many-Chained Molecule Entered tReading 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_04:44:32_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_04:44:33_2013_modification_0.pdb.gz INFO:: moved 181 water molecules 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:: 0.012 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:: 0.073 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_04:44:33_2013_modification_0.pdb.gz Symmetry available for this molecule WARNING:: failed to find master_chain_id "A" in 0 NCS ghosts 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 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 -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 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_04:44:36_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) 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_04:44:37_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 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_04:44:38_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 83 read successfully DEBUG:: there were 0 types with no dictionary 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 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 estcase - Arrange waters round protein PASS: Arrange waters round protein Entered testcase - Correct Segid After Add Terminal Residue PASS: Correct Segid After Add Terminal Residue Entered testcase - Correct Segid after NCS residue range copy PASS: Correct Segid after NCS residue range copy Entered testcase - Merge Water Chains PASS: Merge Water Chains Entered testcase - Consolidated merge -------- starting chain list ----------- DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "") DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K") PASS: Consolidated merge Entered testcase - LSQ by atom PASS: LSQ by atom Entered testcase - LSQing changes the space-group and cell to that of the reference molecule PASS: LSQing changes the space-group and cell to that of the reference molecule Entered testcase - set-residue-name sets the correct residue PASS: set-residue-name sets the correct residue Entered testcase - fit-protein-make-specs makes all specs 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 "")) PASS: fit-protein-make-specs makes all specs Entered testcase - Phosphate distance in pucker analysis is sane PASS: Phosphate distance in pucker analysis is sane Ended 01-pdb+mtz.scm Running 02-shelx.scm ... Entered testcase - Read small molecule .res file PASS: Read small molecule .res file EMolecule 85 read successfully 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 86 read successfully INFO:: spacegroup: I 41 2 2 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 87 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 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. Symmetry available for this molecule 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_04:44:40_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" INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Fri_Sep_13_04:44:40_2013_modification_0.res 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to 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_04:44:40_2013_modification_1.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O " INFO:: Adding to solvent chain: D 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 92 read successfully 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 93 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 94 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 95 read successfully INFO:: Creating directory coot-ccp4 ntered testcase - Read hollander small molecule .res file PASS: Read hollander small molecule .res file Entered testcase - read shelx insulin with fcf PASS: read shelx insulin with fcf Entered testcase - Write an INS from PDB test PASS: Write an INS from PDB test Entered testcase - new molecule by atom selection inherits shelx molecule flag PASS: new molecule by atom selection inherits shelx molecule flag Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy Entered testcase - Add water to SHELX molecule PASS: Add water to SHELX molecule Entered testcase - Find Waters for a SHELXL molecule PASS: Find Waters for a SHELXL molecule Entered testcase - NPD Anisotropic Atom [Mitch Miller] PASS: NPD Anisotropic Atom [Mitch Miller] Entered testcase - close shelx molecules PASS: close shelx molecules Entered testcase - Aniso Bs in P21 b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) PASS: Aniso Bs in P21 Entered testcase - Don't crash on reading a strange HAT file PASS: Don't crash on reading a strange HAT file Ended 02-shelx.scm Running 03-ligand.scm ... Entered testcase - Get monomer test run-command-in-dir args: "coot-ccp4/" "libcheck" () ("N" "MON 3GP" "") "coot-libcheck-3GP.log" #t : : --- LIBCHECK --- /Vers 5.2.00 ; 12.12.2011/ : : : Do you want to have FILE-DOCUMENT /libcheck.doc/ ? //Y/A : : N - means without DOC-file : Y - with new contents : A - means to keep old contents and add new information : with DOC-file program creates batch file: libcheck.bat : _DOC: : : # : # Keywords: : # : #FILE_L: < > - additional library, " " means without this file : #MON: < > - give info about this monomer : # if = * , give list all monomers in the library : #FILE_PDB: < > - input PDB_file ," " means without this file : #FILE_SMILE: < > - input SMILE_file ," " means without this fil e : #FILE_SDF: < > - input SDF file, " " means without this file : #FILE_MOL: < > - input MOL (sybil), SDF, ODB (O) files : # use keyword MON as compound_id : #FILE_CIF: < > - input CIFile ," " means without this file : #FILE_CSD: < > - input CSD CIFile," " means without this file : #HFLAG: /A/N - Y - hydrogen atoms where they are : # A - with all hydrogen atoms : # N - without hydrogen atoms : #IND: /Y - Y - create index of mon_lib.cif : # output file: "new_mon_lib_ind.cif" : #FILE_O: - output files /library,coords,ps/, name without : # extention : #FILE_L2: < > - additional library (FILE_L) will be added to this library : # in this case program performs only adding : #ANGLE: <0.0> - rotation angle for picture ( around X ) : #LIST: /S/L - S short output, L - long, M - medium : #REF: /S,N,0 - 0 no refinement of new monomer : # N only crd->ang and ang->crd : # S plus torsion ref, Y plus restr.ref : # : #TEST: <0> - for program testing only : #COOR: /Y - use Vobs from coords instead Videal : #LCOOR: /N - Y use coords from lib description : #NODIST: /Y - Y not read the distributed library : # (only with FILE_L) : #SRCH: /Y/0 - Y - global search, 0 - for MON from PDB_file : # (only with NODIST = N) : : #--- type "keyword parameters" and/or --- : #--- press key "CR" to run program --- : --> --> MON : 3GP : ------------- : ------------- : Keywords: : HFLAG : Y : COOR : N : LCOOR : Y : SRCH : N : REF : Y : NODIST: N : NUMBER OF MONOMERS IN THE LIBRARY : 11459 : with complete description : 11459 : NUMBER OF MODIFICATIONS : 53 : NUMBER OF LINKS : 66 : I am reading libraries. Please wait. : - energy parameters : - monomer"s description (links & mod ) : I am reading library. Please wait. : - monomer"s description : * CIFile : libcheck_3GP.cif : * PDBfile : libcheck_3GP.pdb : * Plotfile: libcheck_3GP.ps : Output dictionary : mmcif : libcheck.lib : odb : libcheck.odb INFO:: libcheck status: 0 : : :
: : :
: 
: ###############################################################
: ###############################################################
: ###############################################################
: ### CCP4 6.3: Refmac_5.7.0029     version 5.7.0029 : 25/06/12##
: ###############################################################
: User: emsley  Run date: 13/ 9/2013 Run time: 04:44:45 
:
:
: Please reference: Collaborative Computational Project, Number 4. 1994.
: "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
: as well as any specific reference in the program write-up.
:
:
: $TEXT:Reference1: $$ Main reference $$ 
:   "REFMAC5 for the refinement of macromolecular crystal structures:"
:   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
:   Acta Crystallogr. D67, 355-367
:
: $$
: $SUMMARY :Reference1:  $$ Refmac: $$
: :TEXT:Reference1: $$
:
: $TEXT:Reference2: $$ Secondary reference $$ 
:   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
:   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
:   Acta Crystallogr. D53, 240-255
:   EU  Validation contract: BIO2CT-92-0524
:
: $$
: $SUMMARY :Reference2:  $$ Refmac: $$
: :TEXT:Reference2: $$
:
:  Data line--- MODE NEWENTRY
:  Data line--- END
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
:
:    ****                     Input and Default parameters#                      ****
:
:
:Input coordinate file.  Logical name - XYZIN actual file name  - coot-ccp4/libcheck_3GP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name - coot-ccp4/monomer-3GP.pdb
:
:  Refinement type                        : Idealisation
:
:
:    ****                           Makecif parameters                           ****
:
:Dictionary files for restraints : /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif
:User supplied dictionary entries: coot-ccp4/libcheck_3GP.cif
:    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
:    Hydrogens will be restored in their riding positions
:    hydrogens will be written to the output file
:    Links between monomers will be checked. Only those links present in the coordinate file will be used
:    Standard sugar links will be analysed and used
:    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
:    Symmetry related links will be analysed and used
:    Cis peptides will be found and used automatically
:
:
:
:
:Monitoring style is "MEDIUM". Complete information will be printed out in the
:first and last cycle. In all other cycles minimum information will be printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will be printed out
:Distance outliers      10.000
:Angle outliers         10.000
:Torsion outliers       10.000
:Chiral volume outliers 10.000
:Plane outliers         10.000
:Non-bonding outliers   10.000
:---------------------------------------------------------------
:
: Input file :coot-ccp4/libcheck_3GP.pdb
:  NUMBER OF MONOMERS IN THE LIBRARY          : 11459
:                with complete description    : 11459
:  NUMBER OF MODIFICATIONS                    :    53
:  NUMBER OF LINKS                            :    66
:  I am reading libraries. Please wait.
:      - energy parameters
:      - monomer"s description (links & mod )
:
:FORMATTED      OLD     file opened on unit  45
:
:Logical name: ATOMSF, Filename: /home/emsley/ccp4/ccp4-6.3.0/lib/data/atomsf.lib
:
:
:
: Spacegroup information obtained from library file: 
: Logical Name: SYMINFO   Filename: /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/syminfo.lib
:
:  WARNING: "SCALE" card is absent in input PDB file
:  Number of atoms    :      36
:  Number of residues :       1
:  Number of chains   :       1
:  I am reading library. Please wait.
:                mon_lib.cif
:  --------------------------------
:  --- title of input coord file ---
:
:  PDB_code:3GP
:  PDB_name:coords of 3GP from prog: libcheck
:  PDB_date:XX-XXX-XX
:  --------------------------------
:  Number of chains                  :       1
:  Total number of monomers          :       1
:  Number of atoms                   :      36
:  Number of missing atoms           :       0
:  Number of rebuilt atoms           :       0
:  Number of unknown atoms           :       0
:  Number of deleted atoms           :       0
:
:
: loop_
:     _atom_type_symbol
:     _atom_type_scat_Cromer_Mann_a1
:     _atom_type_scat_Cromer_Mann_b1
:     _atom_type_scat_Cromer_Mann_a2
:     _atom_type_scat_Cromer_Mann_b2
:     _atom_type_scat_Cromer_Mann_a3
:     _atom_type_scat_Cromer_Mann_b3
:     _atom_type_scat_Cromer_Mann_a4
:     _atom_type_scat_Cromer_Mann_b4
:     _atom_type_scat_Cromer_Mann_c
:
:
:  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
:  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
:  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
:  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
:  P      6.4345   1.9067   4.1791  27.1570   1.7800   0.5260   1.4908  68.1645   1.1149
:
:
: Number of distances         :           0
: Number of angles            :           0
: Number of torsions          :           0
: Number of planes            :           0
: Number of chirals           :           0
: Number of intervals         :           0
:--------------------------------------------------------------------------------
:---------------------------------------
:                        Standard  External       All
:                Bonds:        38         0        38
:               Angles:        66         0        66
:              Chirals:         4         0         4
:               Planes:         2         0         2
:             Torsions:        22         0        22
:---------------------------------------
:
:
:
:     CGMAT cycle number =      1
:
: function value    19446.416    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.030     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     4.292     3.000
:Bond angles  : others                            26     1.222     3.000
:Torsion angles, period  1. refined               15     3.618    15.000
:Torsion angles, period  1. others                 3     0.015    15.000
:Torsion angles, period  3. refined                4     5.039    15.000
:Chiral centres: refined atoms                     4     0.186     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.005     0.020
:VDW repulsions.others                             6     0.189     0.200
:VDW; torsion: refined_atoms                       7     0.281     0.200
:VDW; torsion.others                               4     0.224     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       19446.416       363.92786       19446.416    
:
:
:     CGMAT cycle number =      2
:
: function value    363.92786    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.081     0.020
:Bond distances: others                           12     0.013     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       363.92786       1259.5922       363.92786    
:
: fvalues    0.0000000       363.92786       483.19171       363.92786    
:
:
:     CGMAT cycle number =      3
:
: function value    343.50781    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.079     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       343.50781       293.11017       343.50781    
:
:
:     CGMAT cycle number =      4
:
: function value    293.11017    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.076     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Gamma decreased to   1.66446306E-02
:
:
: fvalues    0.0000000       293.11017       287.58200       293.11017    
:
:
:     CGMAT cycle number =      5
:
: function value    287.58200    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   1.66446306E-02
: Gamma decreased to   9.13148280E-03
:
:
: fvalues    0.0000000       287.58200       230.52641       287.58200    
:
:
:     CGMAT cycle number =      6
:
: function value    230.52641    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.13148280E-03
: Not converging with gamma equal   9.13148280E-03
: Trying gamma equal   4.66972217E-02
: Gamma decreased to   3.91840748E-02
:
:
: fvalues    0.0000000       230.52641       281.71072       230.52641    
:
: fvalues    0.0000000       230.52641       242.13728       230.52641    
:
:
:     CGMAT cycle number =      7
:
: function value    233.00272    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.91840748E-02
: Gamma decreased to   3.23539414E-02
:
:
: fvalues    0.0000000       233.00272       230.08240       233.00272    
:
:
:     CGMAT cycle number =      8
:
: function value    230.08240    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.23539414E-02
: Gamma decreased to   2.61447281E-02
:
:
: fvalues    0.0000000       230.08240       229.98131       230.08240    
:
:
:     CGMAT cycle number =      9
:
: function value    229.98131    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.61447281E-02
: Gamma decreased to   2.04999894E-02
:
:
: fvalues    0.0000000       229.98131       229.51228       229.98131    
:
:
:     CGMAT cycle number =     10
:
: function value    229.51228    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.04999894E-02
: Not converging with gamma equal   2.04999894E-02
: Trying gamma equal   4.87236828E-02
: Not converging with gamma equal   4.87236828E-02
: Trying gamma equal   7.97697455E-02
: Not converging with gamma equal   7.97697455E-02
: Trying gamma equal   0.11392042    
: Not converging with gamma equal   0.11392042    
: Trying gamma equal   0.15148616    
: Not converging with gamma equal   0.15148616    
: Trying gamma equal   0.19280848    
: Gamma decreased to   0.18454401    
:
:
: fvalues    0.0000000       229.51228       229.47993       229.51228    
:
:
:     CGMAT cycle number =     11
:
: function value    229.47993    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.18454401    
: Gamma decreased to   0.17703086    
:
:
: fvalues    0.0000000       229.47993       229.44974       229.47993    
:
:
:     CGMAT cycle number =     12
:
: function value    229.44974    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17703086    
: Gamma decreased to   0.17020072    
:
:
: fvalues    0.0000000       229.44974       229.42068       229.44974    
:
:
:     CGMAT cycle number =     13
:
: function value    229.42068    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17020072    
: Gamma decreased to   0.16399151    
:
:
: fvalues    0.0000000       229.42068       229.39333       229.42068    
:
:
:     CGMAT cycle number =     14
:
: function value    229.39333    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.16399151    
: Gamma decreased to   0.15834677    
:
:
: fvalues    0.0000000       229.39333       229.36681       229.39333    
:
:
:     CGMAT cycle number =     15
:
: function value    229.36681    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15834677    
: Gamma decreased to   0.15321518    
:
:
: fvalues    0.0000000       229.36681       229.34163       229.36681    
:
:
:     CGMAT cycle number =     16
:
: function value    229.34163    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15321518    
: Gamma decreased to   0.14855011    
:
:
: fvalues    0.0000000       229.34163       229.31769       229.34163    
:
:
:     CGMAT cycle number =     17
:
: function value    229.31769    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14855011    
: Gamma decreased to   0.14430913    
:
:
: fvalues    0.0000000       229.31769       229.29506       229.31769    
:
:
:     CGMAT cycle number =     18
:
: function value    229.29506    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14430913    
: Gamma decreased to   0.14045370    
:
:
: fvalues    0.0000000       229.29506       229.27348       229.29506    
:
:
:     CGMAT cycle number =     19
:
: function value    229.27348    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14045370    
: Gamma decreased to   0.13694876    
:
:
: fvalues    0.0000000       229.27348       229.25328       229.27348    
:
:
:     CGMAT cycle number =     20
:
: function value    229.25328    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13694876    
: Gamma decreased to   0.13376246    
:
:
: fvalues    0.0000000       229.25328       229.23459       229.25328    
:
:
:     CGMAT cycle number =      1
:
: function value    3954.6292    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     3.958     3.000
:Bond angles  : others                            26     1.410     3.000
:Torsion angles, period  1. refined               15     1.476    15.000
:Torsion angles, period  1. others                 3     0.190    15.000
:Torsion angles, period  3. refined                4     7.029    15.000
:Chiral centres: refined atoms                     4     0.035     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             1     0.000     0.200
:VDW; torsion: refined_atoms                       6     0.007     0.200
:VDW; torsion.others                               6     0.000     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       3954.6292       1645.5861       3954.6292    
:
:
:     CGMAT cycle number =      2
:
: function value    1645.5861    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.064     0.020
:Bond distances: others                           12     0.011     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       1645.5861       1504.8378       1645.5861    
:
:
:     CGMAT cycle number =      3
:
: function value    1504.8378    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.054     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       1504.8378       1416.2617       1504.8378    
:
:
:     CGMAT cycle number =      4
:
: function value    1416.2617    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.048     0.020
:Bond distances: others                           12     0.008     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Not converging with gamma equal   2.49090921E-02
: Trying gamma equal   7.03636408E-02
: Gamma decreased to   6.12727329E-02
:
:
: fvalues    0.0000000       1416.2617       1384.2695       1416.2617    
:
:
:     CGMAT cycle number =      5
:
: function value    1384.2695    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.045     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.12727329E-02
: Not converging with gamma equal   6.12727329E-02
: Trying gamma equal   0.10672728    
: Not converging with gamma equal   0.10672728    
: Trying gamma equal   0.15672728    
: Gamma decreased to   0.14672728    
:
:
: fvalues    0.0000000       1384.2695       1370.8711       1384.2695    
:
:
:     CGMAT cycle number =      6
:
: function value    1370.8711    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.045     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14672728    
: Gamma decreased to   0.13763636    
:
:
: fvalues    0.0000000       1370.8711       1358.0048       1370.8711    
:
:
:     CGMAT cycle number =      7
:
: function value    1358.0048    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.044     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13763636    
: Gamma decreased to   0.12937190    
:
:
: fvalues    0.0000000       1358.0048       1345.6464       1358.0048    
:
:
:     CGMAT cycle number =      8
:
: function value    1345.6464    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.043     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12937190    
: Gamma decreased to   0.12185875    
:
:
: fvalues    0.0000000       1345.6464       1333.7854       1345.6464    
:
:
:     CGMAT cycle number =      9
:
: function value    1333.7854    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.043     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12185875    
: Gamma decreased to   0.11502861    
:
:
: fvalues    0.0000000       1333.7854       1322.4045       1333.7854    
:
:
:     CGMAT cycle number =     10
:
: function value    1322.4045    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11502861    
: Gamma decreased to   0.10881940    
:
:
: fvalues    0.0000000       1322.4045       1311.4878       1322.4045    
:
:
:     CGMAT cycle number =     11
:
: function value    1311.4878    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10881940    
: Gamma decreased to   0.10317466    
:
:
: fvalues    0.0000000       1311.4878       1301.0240       1311.4878    
:
:
:     CGMAT cycle number =     12
:
: function value    1301.0240    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10317466    
: Gamma decreased to   9.80430841E-02
:
:
: fvalues    0.0000000       1301.0240       1290.9941       1301.0240    
:
:
:     CGMAT cycle number =     13
:
: function value    1290.9941    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.80430841E-02
: Not converging with gamma equal   9.80430841E-02
: Trying gamma equal   0.12370099    
: Gamma decreased to   0.11856941    
:
:
: fvalues    0.0000000       1290.9941       1283.1353       1290.9941    
:
:
:     CGMAT cycle number =     14
:
: function value    1283.1353    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11856941    
: Gamma decreased to   0.11390433    
:
:
: fvalues    0.0000000       1283.1353       1275.5366       1283.1353    
:
:
:     CGMAT cycle number =     15
:
: function value    1275.5366    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11390433    
: Gamma decreased to   0.10966336    
:
:
: fvalues    0.0000000       1275.5366       1268.1951       1275.5366    
:
:
:     CGMAT cycle number =     16
:
: function value    1268.1951    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10966336    
: Gamma decreased to   0.10580793    
:
:
: fvalues    0.0000000       1268.1951       1261.1099       1268.1951    
:
:
:     CGMAT cycle number =     17
:
: function value    1261.1099    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10580793    
: Gamma decreased to   0.10230299    
:
:
: fvalues    0.0000000       1261.1099       1254.2709       1261.1099    
:
:
:     CGMAT cycle number =     18
:
: function value    1254.2709    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10230299    
: Gamma decreased to   9.91166830E-02
:
:
: fvalues    0.0000000       1254.2709       1247.6791       1254.2709    
:
:
:     CGMAT cycle number =     19
:
: function value    1247.6791    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.91166830E-02
: Gamma decreased to   9.62200388E-02
:
:
: fvalues    0.0000000       1247.6791       1241.3260       1247.6791    
:
:
:     CGMAT cycle number =     20
:
: function value    1241.3260    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.62200388E-02
: Gamma decreased to   9.35867280E-02
:
:
: fvalues    0.0000000       1241.3260       1235.2091       1241.3260    
:
:
:     CGMAT cycle number =      1
:
: function value    74.495377    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:Bond angles  : refined atoms                     40     2.272     3.000
:Bond angles  : others                            26     0.421     3.000
:Torsion angles, period  1. refined               15     5.524    15.000
:Torsion angles, period  1. others                 3    15.708    15.000
:Torsion angles, period  3. refined                4    13.494    15.000
:Chiral centres: refined atoms                     4     0.106     0.200
:Planar groups: refined atoms                     14     0.010     0.020
:Planar groups: others                             6     0.001     0.020
:VDW repulsions.others                             4     0.054     0.200
:VDW; torsion: refined_atoms                       4     0.320     0.200
:VDW; torsion.others                               6     0.092     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       74.495377       28.820347       74.495377    
:
:
:     CGMAT cycle number =      2
:
: function value    28.820347    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.009     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       28.820347       26.893410       28.820347    
:
:
:     CGMAT cycle number =      3
:
: function value    26.893410    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       26.893410       26.455139       26.893410    
:
:
:     CGMAT cycle number =      4
:
: function value    26.455139    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Not converging with gamma equal   2.49090921E-02
: Trying gamma equal   7.03636408E-02
: Gamma decreased to   6.12727329E-02
:
:
: fvalues    0.0000000       26.455139       26.371088       26.455139    
:
:
:     CGMAT cycle number =      5
:
: function value    26.371088    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.12727329E-02
: Not converging with gamma equal   6.12727329E-02
: Trying gamma equal   0.10672728    
: Not converging with gamma equal   0.10672728    
: Trying gamma equal   0.15672728    
: Not converging with gamma equal   0.15672728    
: Trying gamma equal   0.21172729    
: Gamma decreased to   0.20072728    
:
:
: fvalues    0.0000000       26.371088       26.350555       26.371088    
:
:
:     CGMAT cycle number =      6
:
: function value    26.350555    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.20072728    
: Gamma decreased to   0.19072728    
:
:
: fvalues    0.0000000       26.350555       26.334232       26.350555    
:
:
:     CGMAT cycle number =      7
:
: function value    26.334232    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.19072728    
: Gamma decreased to   0.18163636    
:
:
: fvalues    0.0000000       26.334232       26.320751       26.334232    
:
:
:     CGMAT cycle number =      8
:
: function value    26.320751    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.18163636    
: Gamma decreased to   0.17337190    
:
:
: fvalues    0.0000000       26.320751       26.309345       26.320751    
:
:
:     CGMAT cycle number =      9
:
: function value    26.309345    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17337190    
: Gamma decreased to   0.16585875    
:
:
: fvalues    0.0000000       26.309345       26.299595       26.309345    
:
:
:     CGMAT cycle number =     10
:
: function value    26.299595    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.16585875    
: Gamma decreased to   0.15902860    
:
:
: fvalues    0.0000000       26.299595       26.291113       26.299595    
:
:
:     CGMAT cycle number =     11
:
: function value    26.291113    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15902860    
: Gamma decreased to   0.15281940    
:
:
: fvalues    0.0000000       26.291113       26.283710       26.291113    
:
:
:     CGMAT cycle number =     12
:
: function value    26.283710    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15281940    
: Gamma decreased to   0.14717466    
:
:
: fvalues    0.0000000       26.283710       26.277178       26.283710    
:
:
:     CGMAT cycle number =     13
:
: function value    26.277178    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14717466    
: Gamma decreased to   0.14204307    
:
:
: fvalues    0.0000000       26.277178       26.271406       26.277178    
:
:
:     CGMAT cycle number =     14
:
: function value    26.271406    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14204307    
: Gamma decreased to   0.13737799    
:
:
: fvalues    0.0000000       26.271406       26.266275       26.271406    
:
:
:     CGMAT cycle number =     15
:
: function value    26.266275    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13737799    
: Gamma decreased to   0.13313702    
:
:
: fvalues    0.0000000       26.266275       26.261736       26.266275    
:
:
:     CGMAT cycle number =     16
:
: function value    26.261736    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13313702    
: Gamma decreased to   0.12928158    
:
:
: fvalues    0.0000000       26.261736       26.257744       26.261736    
:
:
:     CGMAT cycle number =     17
:
: function value    26.257744    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12928158    
: Gamma decreased to   0.12577665    
:
:
: fvalues    0.0000000       26.257744       26.254160       26.257744    
:
:
:     CGMAT cycle number =     18
:
: function value    26.254160    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12577665    
: Gamma decreased to   0.12259034    
:
:
: fvalues    0.0000000       26.254160       26.250973       26.254160    
:
:
:     CGMAT cycle number =     19
:
: function value    26.250973    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12259034    
: Gamma decreased to   0.11969370    
:
:
: fvalues    0.0000000       26.250973       26.248142       26.250973    
:
:
:     CGMAT cycle number =     20
:
: function value    26.248142    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11969370    
: Gamma decreased to   0.11706039    
:
:
: fvalues    0.0000000       26.248142       26.245613       26.248142    
:  Time in seconds: CPU =         0.48
:             Elapsed =           0.00
:
:    ****           Things for loggraph, R factor and others vs cycle            ****
:
:
:$TABLE: Rfactor analysis, stats vs cycle  :
:$GRAPHS: vs cycle :N:1,2,3:
::FOM vs cycle :N:1,4:
::-LL vs cycle :N:1,5:
::-LLfree vs cycle :N:1,6:
::Geometry vs cycle:N:1,7,8,9,10,11:
:$$
:    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
:$$
:       0   0.0      0.0      0.0           0.       0.0   0.0304  1.521   4.292  1.431   0.186
:       1   0.0      0.0      0.0           0.       0.0   0.0813  4.066   4.676  1.559   0.043
:       2   0.0      0.0      0.0           0.       0.0   0.0794  3.972   4.318  1.439   0.037
:       3   0.0      0.0      0.0           0.       0.0   0.0760  3.798   4.058  1.353   0.017
:       4   0.0      0.0      0.0           0.       0.0   0.0754  3.772   4.010  1.337   0.026
:       5   0.0      0.0      0.0           0.       0.0   0.0754  3.772   3.985  1.328   0.037
:       6   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.981  1.327   0.036
:       7   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.978  1.326   0.036
:       8   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.969  1.323   0.035
:       9   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.965  1.322   0.035
:      10   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      11   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      12   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      13   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      14   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.962  1.321   0.035
:      15   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      16   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      17   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      18   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      19   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.959  1.320   0.035
:      20   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.958  1.319   0.035
:      21   0.0      0.0      0.0           0.       0.0   0.0637  3.184   2.578  0.859   0.088
:      22   0.0      0.0      0.0           0.       0.0   0.0539  2.697   2.487  0.829   0.085
:      23   0.0      0.0      0.0           0.       0.0   0.0477  2.384   2.425  0.808   0.093
:      24   0.0      0.0      0.0           0.       0.0   0.0455  2.273   2.401  0.800   0.098
:      25   0.0      0.0      0.0           0.       0.0   0.0446  2.229   2.391  0.797   0.100
:      26   0.0      0.0      0.0           0.       0.0   0.0438  2.191   2.380  0.793   0.101
:      27   0.0      0.0      0.0           0.       0.0   0.0432  2.158   2.370  0.790   0.102
:      28   0.0      0.0      0.0           0.       0.0   0.0426  2.128   2.360  0.787   0.103
:      29   0.0      0.0      0.0           0.       0.0   0.0420  2.102   2.351  0.784   0.104
:      30   0.0      0.0      0.0           0.       0.0   0.0416  2.079   2.341  0.780   0.105
:      31   0.0      0.0      0.0           0.       0.0   0.0412  2.058   2.332  0.777   0.106
:      32   0.0      0.0      0.0           0.       0.0   0.0408  2.040   2.323  0.774   0.106
:      33   0.0      0.0      0.0           0.       0.0   0.0405  2.026   2.316  0.772   0.107
:      34   0.0      0.0      0.0           0.       0.0   0.0403  2.013   2.309  0.770   0.107
:      35   0.0      0.0      0.0           0.       0.0   0.0400  2.000   2.302  0.767   0.107
:      36   0.0      0.0      0.0           0.       0.0   0.0398  1.989   2.296  0.765   0.107
:      37   0.0      0.0      0.0           0.       0.0   0.0396  1.978   2.290  0.763   0.107
:      38   0.0      0.0      0.0           0.       0.0   0.0394  1.968   2.283  0.761   0.107
:      39   0.0      0.0      0.0           0.       0.0   0.0392  1.958   2.277  0.759   0.106
:      40   0.0      0.0      0.0           0.       0.0   0.0390  1.949   2.272  0.757   0.106
:      41   0.0      0.0      0.0           0.       0.0   0.0087  0.435   2.793  0.931   0.046
:      42   0.0      0.0      0.0           0.       0.0   0.0070  0.349   2.801  0.934   0.036
:      43   0.0      0.0      0.0           0.       0.0   0.0065  0.327   2.808  0.936   0.034
:      44   0.0      0.0      0.0           0.       0.0   0.0065  0.324   2.810  0.937   0.034
:      45   0.0      0.0      0.0           0.       0.0   0.0065  0.323   2.810  0.937   0.034
:      46   0.0      0.0      0.0           0.       0.0   0.0064  0.322   2.810  0.937   0.034
:      47   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.810  0.937   0.034
:      48   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.810  0.937   0.034
:      49Reading 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 96 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_04:44:53_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_04:44:53_2013_modification_1.pdb.gz
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 97 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
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 98 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 
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 99 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 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:44:53_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 
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 100 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 106 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:: 0.136 seconds to read MTZ file
INFO:: 0.098 seconds to initialize map
INFO:: 0.071 seconds for FFT
INFO:: 0.007 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:: 0.32 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:: 0.078 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.071 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:: 0.159 seconds in total
Executing ligand search...
INFO:: ligand number 0 is molecule number 100   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
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 125 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_04:45:04_2013_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:45:04_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_04:45:04_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_04:45:04_2013_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
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 127 read successfully
DEBUG:: there were 0 types with no dictionary 
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
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 128 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 128
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 128
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 129 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:: 0.001 seconds to initialize map
INFO:: 0.015 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 129

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_04:45:07_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.
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_04:45:07_2013_modification_0.pdb.gz
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: Matching/moving molecule number 133 to 133
ERROR:: No symmetry available
INFO:: LSQ matched 125 atoms
INFO:: 125 matched atoms had: 
   mean devi: 0.141862
    rms devi: 0.1486
    max devi: 0.243105
    min devi: 0.0283178
INFO:: Axis orientation: (    0.3864,   -0.6781,   -0.6252)
INFO:: Rotation in CCP4 Polar Angles: Polar = (128.694,-60.3228,0.295209)
INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Fri_Sep_13_04:45:08_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|         1,  0.003218, -0.003497|
| -0.003225,         1, -0.001985|
|  0.003491,  0.001997,         1|
(    -24.05,     -23.7,    -24.44)
No unit cell for this molecule, hence no fractional matrix.
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 134 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 135 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 134 has 750 atoms selected
INFO:: moving    135 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_04:45:09_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%
Error reading /home/emsley/data/greg-data/1pyd.pdb
   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.809  0.936   0.034
:      50   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.809  0.936   0.034
:      51   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      52   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      53   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      54   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      55   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      56   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      57   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
:      58   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
:      59   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:
: Refmac_5.7.0029:  End of Refmac_5.7.0029 
:Times: User:       8.1s System:    0.4s Elapsed:     0:08  
:
: : INFO:: libcheck-minimal? is #f PASS: Get monomer test Entered testcase - Set Bond thickness PASS: Set Bond thickness Entered testcase - Delete all-molecule Hydrogens here 1 PASS: Delete all-molecule Hydrogens Entered testcase - Non-Autoloads PASS: Non-Autoloads Entered testcase - Move and Refine Ligand test PASS: Move and Refine Ligand test Entered testcase - Many Molecules - Ligand Fitting Fitting NPO gave these results: (110 111 112 113 114 115 116 117 118 119 120 121 122 123 124) PASS: Many Molecules - Ligand Fitting Entered testcase - flip residue (around eigen vectors) distance: 4.35071918939919 distance d2: 1.19209289550781e-7 PASS: flip residue (around eigen vectors) Entered testcase - Test dipole info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0) PASS: Test dipole Entered testcase - Reading new dictionary restraints replaces PASS: Reading new dictionary restraints replaces Ended 03-ligand.scm Running 04-cootaneer.scm ... Entered testcase - Assignment of new PIR sequence overwrites old assignment debug seq: ("A" . "ACDEFGHIKLMNPQ") PASS: Assignment of new PIR sequence overwrites old assignment Entered testcase - Cootaneer Beta Strand Cootaneering: imol 129 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" PASS: Cootaneer Beta Strand Ended 04-cootaneer.scm Running 05-rna-ghosts.scm ... Entered testcase - RNA NCS Ghosts There are 8 residues in chain "A" There are 8 residues in chain "B" PASS: RNA NCS Ghosts Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example PASS: SSM - Frank von Delft's Example Entered testcase - SSM - Alice Dawson's Example 0 "/home/emsley/data/greg-data/tutorial-modern.pdb" 2 "/home/emsley/data/greg-data/ins-code-fragment-pre.pdb" 3 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 4 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 5 "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 6 "test-3hfl.map" 7 "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 8 "atom selection from tutorial-add-terminal-1-test.pdb" 9 "/home/emsley/data/greg-data/frag-2wot.pdb" 10 "sphere selection from tutorial-modern.pdb" 12 "/home/emsley/data/greg-data/rotamer-test-fragment.pdb" 13 "/home/emsley/data/greg-data/res098.pdb" 14 "/home/emsley/data/greg-data/tutorial-modern.pdb" 15 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 16 "/home/emsley/data/greg-data/pdb3knw.ent" 19 "/home/emsley/data/greg-data/alt-conf-pepflip-test.pdb" 20 "/home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 21 "/home/emsley/data/greg-data/tutorial-modern.pdb" 22 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 23 "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 24 "/home/emsley/data/greg-data/tutorial-modern.pdb" 25 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 26 "/home/emsley/data/greg-data/alt-conf-waters.pdb" 27 "/home/emsley/data/greg-data/backrub-fragment.pdb" 28 "Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb" 29 "/home/emsley/data/greg-data/coords-B3A.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 "/home/emsley/data/greg-data/HOF.RES" 86 "/home/emsley/data/greg-data/hollander.ins" 89 "/home/emsley/data/greg-data/insulin.fcf" 90 "atom selection from insulin.res" 91 "atom selection from insulin.res" 93 "/home/emsley/data/greg-data/horma-p21.res" 94 "new-horma.ins" 95 "/home/emsley/data/greg-data/crash.hat" 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 136 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 137 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 136 has 169 atoms selected INFO:: moving 137 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_04:45:11_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% 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 138 read successfully 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:: 0.026 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:: 0.062 seconds in total INFO:: NCS chain comparison 93/93 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 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) 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 3 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2 maps contributing to the average INFO:: rescaling by 0.5 INFO:: 737280 out of 737280 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.00029312 st.d: 0.325007 Map statistics: min: -1.48938, max: 2.40191 -1.3921 10 -1.19753 23 -1.00297 78 -0.808402 1162 -0.613838 12942 -0.419273 80812 -0.224709 194625 -0.0301443 193759 0.16442 117773 0.358985 67091 0.553549 36147 0.748113 18238 0.942678 8655 1.13724 3780 1.33181 1483 1.52637 485 1.72094 128 1.9155 65 2.11006 18 2.30463 6 2.49919 0 INFO:: installing ghost map with name :Map 139 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2 maps contributing to the average INFO:: rescaling by 0.5 INFO:: 228096 out of 228096 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.000355333 st.d: 0.323619 Map statistics: min: -1.44957, max: 2.34115 -1.3548 4 -1.16527 12 -0.975731 37 -0.786195 453 -0.596659 4596 -0.407123 26403 -0.217587 59478 -0.0280513 58289 0.161485 36006 0.351021 20752 0.540556 11414 0.730092 5769 0.919628 2875 1.10916 1265 1.2987 484 1.48824 176 1.67777 54 1.86731 20 2.05684 7 2.24638 2 2.43592 0 no diffs NCS target chain has 93 peers. 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 144 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_04:45:14_2013_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_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_04:45:14_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_04:45:14_2013_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_5.pdb.gz 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 145 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_04:45:15_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_04:45:15_2013_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Fri_Sep_13_04:45:15_2013_modification_2.pdb.gz 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 146 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 146 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 147 to 146 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_04:45:18_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) Symmetry available for this molecule INFO:: Matching/moving molecule number 148 to 146 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: ( -0.431, 0.3986, 0.8095) INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:45:18_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.6203, -0.2279, -0.7505| | -0.4559, -0.6739, 0.5814| | -0.6382, 0.7028, 0.3141| ( -22.14, -19.93, 1.626) INFO:: fractional coordinates matrix: | -0.8835, -0.09252, -0.543| | -0.5264, -0.4107, 0.8789| | -0.4875, 0.7087, 0.3141| ( -0.381, -0.2605, 0.01406) Symmetry available for this molecule INFO:: Matching/moving molecule number 149 to 146 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: ( 0.6231, -0.7786, -0.07411) INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:45:18_2013_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) 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:: 0.039 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:: 0.099 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 error (syntax error) error (syntax error) error (not syntax error) Traceback (most recent call last): File "", line 1, in NameError: name 'rr_not_found_thing' is not defined 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 160 read successfully DEBUG:: there were 0 types with no dictionary Entering test: OXT in restraints? 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 There are 2 data in /home/emsley/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.141421 PASS: test symm trans to origin Entering test: test lsq plane LSQ deviations: 0 1.22483e-17 PASS: test lsq plane Entering test: test COO modification 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/data/greg-data/hideous-OXT.pdb PDB file /home/emsley/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom created 7 bond restraints created 8 angle restraints created 1 plane restraints created 1 chiral vol restraints created 2 torsion restraints created 23 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 93 and 93 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: 10113.4 Initial RMS Z values bonds: 3.72079 angles: 7.46884 torsions: 0.276426 planes: 16.9011 non-bonded: 221.797 chiral vol: 1.22665 rama plot: N/A start_pos: N/A Minimum found (iteration number 946) at 24.2085 Final Estimated RMS Z Scores: bonds: 1.14991 angles: 1.01461 torsions: 0.0248459 planes: 0.00133524 non-bonded: 0.0833607 chiral vol: 0.00317726 rama plot: N/A start_pos: N/A refinement_took 0.022 seconds OXT out of plane distance: 7.81835e-05 OXT->O distance: 2.27418 PASS: test COO modification Entering test: remove whitespace PASS: remove whitespace Entering test: Residues for phi,psi are close enough to be considered linked 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 bad residues for phi,psi calculation bad residues for phi,psi calculation PASS: Residues for phi,psi are close enough to be considered linked 96 "coot-ccp4/monomer-3GP.pdb" 97 "/home/emsley/data/greg-data/monomer-3GP.pdb" 98 "/home/emsley/data/greg-data/test-LIG.pdb" 99 "/home/emsley/data/greg-data/test-LIG.pdb" 100 "/home/emsley/data/greg-data/monomer-NPO.pdb" 101 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 102 "Copy_of_/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 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 107 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 108 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 109 "Masked (by protein)" 110 "Fitted ligand #0-0" 111 "Fitted ligand #0-1" 112 "Fitted ligand #1-0" 113 "Fitted ligand #1-1" 114 "Fitted ligand #2-0" 115 "Fitted ligand #2-1" 116 "Fitted ligand #2-2" 117 "Fitted ligand #3-0" 118 "Fitted ligand #4-0" 119 "Fitted ligand #5-0" 120 "Fitted ligand #6-0" 121 "Fitted ligand #7-0" 122 "Fitted ligand #8-0" 123 "Fitted ligand #9-0" 124 "Fitted ligand #9-1" 125 "coot-ccp4/monomer-3GP.pdb" 126 "Copy_of_coot-ccp4/monomer-3GP.pdb" 127 "/home/emsley/data/greg-data/dipole-residues.pdb" 128 "/home/emsley/data/greg-data/tutorial-modern.pdb" 129 "/home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb" 130 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 131 "Ideal-A-form-RNA" 134 "/home/emsley/data/greg-data/1wly.pdb" 135 "/home/emsley/data/greg-data/1yb5.pdb" PASS: SSM - Alice Dawson's Example Entered testcase - SSM by atom selection [JED Example] PASS: SSM by atom selection [JED Example] Ended 06-ssm.scm Running 07-ncs.scm ... Entered testcase - NCS maps test PASS: NCS maps test Entered testcase - NCS chains info NCS info: (("A" "B")) PASS: NCS chains info Entered testcase - NCS deviation info PASS: NCS deviation info Entered testcase - NCS Residue Range copy PASS: NCS Residue Range copy Entered testcase - NCS Residue Range edit to all chains result: (#t #t) PASS: NCS Residue Range edit to all chains Entered testcase - Manual NCS ghosts generates correct NCS chain ids NCS ghost chain IDs pre: (("B" "A" "C" "D")) NCS ghost chain IDs post: (("B" "A" "C" "D")) PASS: Manual NCS ghosts generates correct NCS chain ids Entered testcase - NCS maps overwrite existing maps ==== test-name: "Map 151 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 151 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 151 NCS found from matching Chain D onto Chain A" n-matchers: 2 PASS: NCS maps overwrite existing maps Ended 07-ncs.scm Running 08-utils.scm ... Entered testcase - Test key symbols WARNING:: could not find key-sym-code for "missing key" PASS: Test key symbols Entered testcase - Test running a Python function test_val_2 passed test_val_3 passed PASS: Test running a Python function Entered testcase - Internal/External Molecule Numbers match PASS: Internal/External Molecule Numbers match Entered testcase - spacegroup operators to space group conversion PASS: spacegroup operators to space group conversion Ended 08-utils.scm Running 09-internal.scm ... Entered testcase - Test internal functions PASS: Test internal functions Ended 09-internal.scm === greg-tests Summary === # of testcases attempted 114 # of expected passes 114 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 === Summary of all tests === # of tools 1 # of testcases attempted 114 # of expected passes 114 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 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. test_coot: coot test passed