testing with python unittest testing with python unittest currently we are here: /home/paule/autobuild/building/emsley-vm-ubuntu1404_2018-09-19__T10_36_02/coot-0.8.9.2-pre /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/bin/coot --no-graphics --script python-tests/coot_unittest.py INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ INFO:: Reading coordinate file: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-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) INFO:: coot.py imported Running python script /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Morning Paul, Welcome to Coot version 0.8.9.2-pre (set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.8.9.2-pre") (use-graphics-interface-state) (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good morning root. Welcome to Coot 0.8.9.2-pre") (set-display-lists-for-maps 0) (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run python-tests/coot_unittest.py Running python script python-tests/coot_unittest.py =============================================================== ==================== Testing ================================== =============================================================== WARNING:: unittest skip not avaliable!!!!!! INFO:: Command: (set-density-size 4.50) ==== It seems CCP4_MASTER is setup === ==== CCP4_MASTER: /home/paule/ccp4 test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... INFO:: Command: (post-go-to-atom-window) ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... INFO:: Command: (close-molecule -2) ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... Molecule number -5 is not a valid model molecule ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2WF6.pdb" 1) WARNING:: Error reading /home/paule/data/greg-data/2WF6.pdb closing molecule number -1 INFO:: Command: (close-molecule -1) ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Command: (info-dialog "Oops! failed to create fragment. No atoms selected Incorrect atom specifier? "//A/100"") INFO:: pre_n_molecules 1 post_n_molecules 1 ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/ins-code-fragment-pre.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/paule/data/greg-data/ins-code-fragment-pre.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 1 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (set-go-to-atom-molecule 1) INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Wed_Sep_19_11:45:10_2018_modification_0.pdb.gz INFO:: Command: (change-residue-number 1 "A" 68 "" 68 "A") INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Wed_Sep_19_11:45:10_2018_modification_1.pdb.gz INFO:: Command: (change-residue-number 1 "A" 69 "" 68 "B") INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Wed_Sep_19_11:45:10_2018_modification_2.pdb.gz INFO:: Command: (change-residue-number 1 "A" 67 "" 68 "") pre and post ins codes: A INFO:: Command: (write-pdb-file 1 "post-ins-change.pdb") pass: ['A', 68, '', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'A', ' CA '] pass: ['A', 68, '', ' CA '] pass: ['A', 66, '', ' CA '] ok test05_1 (__main__.PdbMtzTestFunctions) Replace Residue gets correct residue number ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 2 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (n-chains 0) INFO:: Command: (n-chains 1) INFO:: Command: (n-chains 2) WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:45:10_2018_modification_0.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:45:10_2018_modification_1.pdb.gz INFO:: Command: (delete-residue-hydrogens 3 "A" 1 "" "") INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:45:10_2018_modification_2.pdb.gz INFO:: Command: (delete-atom 3 "A" 1 "" " OXT" "") INFO:: match.MatchGraphs must match at least 9 atoms. INFO:: match NumberofMatches (potentially similar graphs) 2 INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:45:10_2018_modification_3.pdb.gz INFO:: coordinates transformed_by: | -0.08424, 0.8319, -0.5485| | 0.9477, -0.1032, -0.302| | -0.3079, -0.5453, -0.7797| ( 58.88, -22.95, 43.83) INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:45:10_2018_modification_4.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:45:10_2018_modification_5.pdb.gz INFO:: match.MatchGraphs must match at least 9 atoms. INFO:: match NumberofMatches (potentially similar graphs) 2 WARNING:: in torsion match() quad moving not all non-blank ------ after matching, check the torsions torsion check: ( N CA CB CG ) was -60.01 should be -47.18 and is -47.18 torsion check: ( CA CB CG CD2) was -90.31 should be -56.84 and is -56.84 INFO:: rotated 2 torsions in matching torsions INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:10_2018_modification_0.pdb.gz INFO:: Command: (delete-residue 2 "A" 86 "") INFO:: new_chain_id_info: [1, [True, 'A', 101, '']] BL DEBUG:: new res spec [True, 'A', 101, ''] INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:10_2018_modification_1.pdb.gz INFO:: Command: (change-residue-number 2 "A" 101 "" 86 "") INFO:: created 40 restraints created 16 bond restraints created 22 angle restraints created 1 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 433 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 10382.85 Initial RMS Z values bonds: 6.88 angles: 11.49 torsions: N/A planes: 11.88 non-bonded: 11.80 chiral vol: 0.26 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 147) at 55.45 Final Estimated RMS Z Scores: bonds: 0.41 angles: 1.26 torsions: N/A planes: 0.57 non-bonded: 0.00 chiral vol: 2.33 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 0.00 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:10_2018_modification_2.pdb.gz INFO:: replace_coords: 16 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it C-N dist good enough: 1.33569806245 ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... WARNING:: Error reading bogus.map Read map bogus.map failed ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... WARNING:: Can't find file bogus.mtz INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.04 seconds to read MTZ file INFO:: 0.02 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.09 seconds in total ok test07_1 (__main__.PdbMtzTestFunctions) Auto-read bad MTZ test ... WARNING:: file xx-missing.mtz does not exist got status: () >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz got status: () ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... INFO:: map sigmas 0.311501026154 False ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... INFO:: making conventional map from MTZ filename /home/paule/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 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: Command: (another-level-from-map-molecule-number 4) ok test09_1 (__main__.PdbMtzTestFunctions) db-main makes mainchain ... INFO:: Command: (handle-read-draw-molecule-with-recentre "." 1) WARNING:: Error reading . . is a directory. INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 6 read successfully DEBUG:: there were 0 types with no dictionary /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. ERROR 42 READ: Duplicate sequence number and insertion code. LINE #868 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb INFO:: 8375 fragments found in total of which 0 were 5 peptides not backwards A contains 94 residues from 1 to 93 target fragment start res: 10 had 29 db fragment hits, ilength=6 target fragment start res: 13 had 1772 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 16 merge fragments 10 to 20 with 2 fit sets to merge The merging is complete mainchain_fragment from 10 to 20 done mainchain_fragment successfully set cell and symmetry INFO:: Command: (db-mainchain 6 "A" 10 20 "forward") ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... INFO:: Command: (set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.50) ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/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 in add_molecular_symmetry_matrices() made 0 biomt matrices 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 8 read successfully DEBUG:: there were 0 types with no dictionary fitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 1 offset: -1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Sep_19_11:45:11_2018_modification_0.pdb.gz INFO:: Command: (add-terminal-residue 8 "A" 1 1) INFO:: Command: (write-pdb-file 8 "regression-test-terminal-residue.pdb") INFO:: Command: (handle-read-draw-molecule-with-recentre "regression-test-terminal-residue.pdb" 1) INFO:: Reading coordinate file: regression-test-terminal-residue.pdb PDB file regression-test-terminal-residue.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 83/91 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 9 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/atom_selection_from_regression-test-terminal-residue.pdb_Wed_Sep_19_11:45:12_2018_modification_0.pdb.gz INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/frag-2wot.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 11 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 ok test11_2 (__main__.PdbMtzTestFunctions) Add Terminal Residue O Position ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 12 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: Command: (backup-state 12) INFO:: Command: (turn-off-backup 12) fitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: Command: (add-terminal-residue 12 "A" 93 1) Add terminal residue bond check dd_1 0.149976123291 Add terminal residue bond check dd_2 2.25586183574 INFO:: Command: (turn-on-backup 12) ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... INFO:: Command: (n-chains 14) INFO:: Command: (chain_id 14 0) Sphere mol: there are 4 residues in chain B INFO:: Command: (resname-from-serial-number 14 "B" 0) INFO:: Command: (seqnum-from-serial-number 14 "B" 0) INFO:: Command: (insertion-code-from-serial-number 14 "B" 0) INFO:: Command: (resname-from-serial-number 14 "B" 1) INFO:: Command: (seqnum-from-serial-number 14 "B" 1) INFO:: Command: (insertion-code-from-serial-number 14 "B" 1) INFO:: Command: (resname-from-serial-number 14 "B" 2) INFO:: Command: (seqnum-from-serial-number 14 "B" 2) INFO:: Command: (insertion-code-from-serial-number 14 "B" 2) INFO:: Command: (resname-from-serial-number 14 "B" 3) INFO:: Command: (seqnum-from-serial-number 14 "B" 3) INFO:: Command: (insertion-code-from-serial-number 14 "B" 3) Found 20 sphere atoms ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... INFO:: Command: (go-to-view-number 0 1) ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 15 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:12_2018_modification_0.pdb.gz INFO:: Command: (delete-residue 15 "A" 42 "") residue info (should be False): False ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (set-rotation-centre 31.46 21.41 14.82) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:12_2018_modification_0.pdb.gz INFO:: Command: (delete-residue 16 "B" 10 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:12_2018_modification_1.pdb.gz INFO:: Command: (delete-residue 16 "B" 11 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:12_2018_modification_2.pdb.gz INFO:: Command: (delete-residue 16 "B" 12 "") ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/rotamer-test-fragment.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/rotamer-test-fragment.pdb PDB file /home/paule/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 17 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] ok test15_1 (__main__.PdbMtzTestFunctions) HIS with unusual atom order rotates correct fragment for 180 sidechain flip ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/eleanor-HIS.pdb" 1) WARNING:: Error reading /home/paule/data/greg-data/eleanor-HIS.pdb FAIL test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/res098.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/res098.pdb PDB file /home/paule/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 18 read successfully DEBUG:: there were 0 types with no dictionary For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 INFO:: created 19 restraints created 10 bond restraints created 8 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 7 angle links 5 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 129 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 599.33 Initial RMS Z values bonds: 0.20 angles: 0.41 torsions: N/A planes: 0.50 non-bonded: 4.43 chiral vol: 0.16 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 239) at 9.99 Final Estimated RMS Z Scores: bonds: 0.07 angles: 0.62 torsions: N/A planes: 0.60 non-bonded: 0.00 chiral vol: 0.59 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 2.19 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz INFO:: replace_coords: 11 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 19 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:13_2018_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.93 INFO:: Command: (auto-fit-best-rotamer 93 "A" "" "A" 19 20 1 0.01) ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb3knw.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3knw.ent PDB file /home/paule/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links in add_molecular_symmetry_matrices() made 1 biomt matrices 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 21 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3knw.ent_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz se_1: [['SE ', ''], [0.7, 2.0, 'SE', ''], [58.8, 66.533, 0.047], 652] se_2: [['SE ', ''], [0.7, 2.0, 'SE', ''], [60.13112002923666, 69.34847968524429, -0.673518803101735], 652] ok test16_3 (__main__.PdbMtzTestFunctions) Hs are correctly swapped on a TYR ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1py3.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices 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 22 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1py3.ent_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP INFO:: 25 residues had their atoms swapped BL DEBUG:: results: [True, True, True, True] ok test16_4 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 23 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: Command: (zero-occupancy-residue-range 23 "A" 37 37) DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 INFO:: Command: (close-molecule 23) INFO:: Command: (close-molecule 24) ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/paule/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 in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 25 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-pepflip-test.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/paule/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 in add_molecular_symmetry_matrices() made 0 biomt matrices 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 26 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (go-to-view-number 1 1) omega: 1 12.77 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:45:13_2018_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:45:13_2018_modification_2.pdb.gz INFO:: Command: (mutate 26 "A" 11 "" "GLY") INFO:: created 21 restraints created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 1 bond links 4 angle links 3 plane links 1 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 7 angle links 5 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 138 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 4729.19 Initial RMS Z values bonds: 15.46 angles: 7.12 torsions: N/A planes: 1.90 non-bonded: 29.01 chiral vol: 3.04 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 106) at -4887.24 Final Estimated RMS Z Scores: bonds: 0.87 angles: 0.76 torsions: N/A planes: 2.21 non-bonded: 0.06 chiral vol: 0.35 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 2.75 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:45:13_2018_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:45:13_2018_modification_4.pdb.gz INFO:: Command: (mutate 26 "A" 11 "" "LEU") ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:45:13_2018_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.68 INFO:: Command: (auto-fit-best-rotamer 11 "" "" "A" 26 4 1 1.00) ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: created 32 restraints created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints Link restraints: 1 bond links 4 angle links 3 plane links 1 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 7 angle links 5 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 222 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -6033.28 Initial RMS Z values bonds: 0.89 angles: 1.60 torsions: N/A planes: 2.65 non-bonded: 0.22 chiral vol: 0.40 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -6162.16 Final Estimated RMS Z Scores: bonds: 0.86 angles: 0.70 torsions: N/A planes: 2.26 non-bonded: 0.04 chiral vol: 0.21 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 2.83 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:45:13_2018_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Command: (write-pdb-file 26 "tmp-fixed-cis.pdb") ok test18_1 (__main__.PdbMtzTestFunctions) H on a N moves on cis-trans convert ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz cliquize 12 spinables for altconf --------------------------- 12 cliques ---------------- INFO:: Command: (backup-state 28) INFO:: Command: (turn-off-backup 28) omega: 1 -177.75 degrees INFO This is a TRANS peptide - making it CIS INFO:: Command: (turn-on-backup 28) INFO:: Command: (close-molecule 27) INFO:: Command: (close-molecule 28) dd: 3.29414373281 ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 29 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: created 11 restraints created 6 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 80 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -3224.84 Initial RMS Z values bonds: 2.07 angles: 1.07 torsions: N/A planes: 0.61 non-bonded: 3.42 chiral vol: 1.46 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 75) at -3460.95 Final Estimated RMS Z Scores: bonds: 1.01 angles: 1.31 torsions: N/A planes: 0.24 non-bonded: 0.31 chiral vol: 1.23 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.00 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it refined moved: d= 0.105058388151 ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/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 in add_molecular_symmetry_matrices() made 0 biomt matrices 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 31 read successfully DEBUG:: there were 0 types with no dictionary DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Sep_19_11:45:13_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 INFO:: Command: (set-go-to-atom-molecule 31) imol: 31 residues: [['A', 93, ''], ['A', 92, ''], ['A', 3, ''], ['A', 5, '']] INFO:: created 81 restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints FAIL close enough with closer than dist_crit 3.48 FAIL close enough with closer than dist_crit 3.48 FAIL close enough with closer than dist_crit 3.48 FAIL close enough with closer than dist_crit 3.48 FAIL close enough with closer than dist_crit 3.52 FAIL close enough with closer than dist_crit 3.52 FAIL close enough with closer than dist_crit 3.52 FAIL close enough with closer than dist_crit 3.52 FAIL close enough with closer than dist_crit 3.90 FAIL close enough with closer than dist_crit 3.90 FAIL close enough with closer than dist_crit 3.90 FAIL close enough with closer than dist_crit 3.90 Link restraints: 2 bond links 6 angle links 0 plane links 4 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 5 bond links 15 angle links 10 plane links 5 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 1543 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -15829.74 Initial RMS Z values bonds: 1.74 angles: 1.27 torsions: N/A planes: 0.84 non-bonded: 0.00 chiral vol: 0.89 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -16198.21 Final Estimated RMS Z Scores: bonds: 0.93 angles: 0.62 torsions: N/A planes: 0.59 non-bonded: 0.00 chiral vol: 0.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.10 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Sep_19_11:45:13_2018_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it imol: 31 residues: [['A', 41, ''], ['A', 42, ''], ['A', 40, ''], ['A', 39, ''], ['A', 43, '']] INFO:: created 84 restraints created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints FAIL close enough with closer than dist_crit 3.27 FAIL close enough with closer than dist_crit 3.27 FAIL close enough with closer than dist_crit 3.27 FAIL close enough with closer than dist_crit 3.27 FAIL close enough with closer than dist_crit 3.37 FAIL close enough with closer than dist_crit 3.37 FAIL close enough with closer than dist_crit 3.37 FAIL close enough with closer than dist_crit 3.37 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 Link restraints: 4 bond links 12 angle links 8 plane links 3 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 1247 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -7315.05 Initial RMS Z values bonds: 0.98 angles: 1.02 torsions: N/A planes: 1.79 non-bonded: 5.30 chiral vol: 10.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 60) at -15843.90 Final Estimated RMS Z Scores: bonds: 1.99 angles: 1.87 torsions: N/A planes: 1.56 non-bonded: 0.05 chiral vol: 1.82 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.21 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Sep_19_11:45:13_2018_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ======= got bond length 1.28869588415 ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 32 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: created 67 restraints created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 868 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -3137.53 Initial RMS Z values bonds: 0.94 angles: 1.06 torsions: N/A planes: 1.98 non-bonded: 7.48 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 35) at -11537.14 Final Estimated RMS Z Scores: bonds: 2.02 angles: 2.05 torsions: N/A planes: 1.69 non-bonded: 0.07 chiral vol: 2.10 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.39 Refinement elapsed time: 0.06 refinement results: ['', 0, [['Bonds', 'Bonds: 2.018', 2.0175511837005615], ['Angles', 'Angles: 2.047', 2.0469608306884766], ['Planes', 'Planes: 1.691', 1.6905479431152344], ['Non-bonded', 'Non-bonded: 0.257', 0.2571920156478882], ['Chirals', 'Chirals: 2.099', 2.0989038944244385]]] :::: ow factor 1.96349096298 INFO:: setting refinement weight to 15.5630042792 from 60.0 / ( 1.96349096298 * 1.96349096298 ) ---------------------------------------------- ---------------------------------------------- ERROR:: A: last_restraints no cleared up ---------------------------------------------- ---------------------------------------------- INFO:: created 67 restraints created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 868 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 4890.24 Initial RMS Z values bonds: 0.94 angles: 1.06 torsions: N/A planes: 1.98 non-bonded: 7.48 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 69) at -2814.01 Final Estimated RMS Z Scores: bonds: 0.78 angles: 1.40 torsions: N/A planes: 1.83 non-bonded: 0.02 chiral vol: 1.24 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.56 Refinement elapsed time: 0.16 refinement results: ['', 0, [['Bonds', 'Bonds: 0.785', 0.7846631407737732], ['Angles', 'Angles: 1.397', 1.3972275257110596], ['Planes', 'Planes: 1.834', 1.8338701725006104], ['Non-bonded', 'Non-bonded: 0.137', 0.13665597140789032], ['Chirals', 'Chirals: 1.244', 1.2441929578781128]]] :::: ow factor 1.31498844922 INFO:: setting refinement weight to 9.00014625281 from 15.5630044937 / ( 1.31498844922 * 1.31498844922 ) ---------------------------------------------- ---------------------------------------------- ERROR:: A: last_restraints no cleared up ---------------------------------------------- ---------------------------------------------- INFO:: created 67 restraints created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 868 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 6075.85 Initial RMS Z values bonds: 0.94 angles: 1.06 torsions: N/A planes: 1.98 non-bonded: 7.48 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -1554.33 Final Estimated RMS Z Scores: bonds: 0.59 angles: 1.27 torsions: N/A planes: 1.82 non-bonded: 0.01 chiral vol: 1.07 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.65 Refinement elapsed time: 0.09 refinement results: ['', 0, [['Bonds', 'Bonds: 0.595', 0.5948469042778015], ['Angles', 'Angles: 1.273', 1.2726705074310303], ['Planes', 'Planes: 1.823', 1.8234121799468994], ['Non-bonded', 'Non-bonded: 0.109', 0.1090817004442215], ['Chirals', 'Chirals: 1.068', 1.06765615940094]]] :::: ow factor 1.18964643776 INFO:: setting refinement weight to 6.35936472247 from 9.00014591217 / ( 1.18964643776 * 1.18964643776 ) ---------------------------------------------- ---------------------------------------------- ERROR:: A: last_restraints no cleared up ---------------------------------------------- ---------------------------------------------- INFO:: created 67 restraints created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 868 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 6552.92 Initial RMS Z values bonds: 0.94 angles: 1.06 torsions: N/A planes: 1.98 non-bonded: 7.48 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 54) at -1060.03 Final Estimated RMS Z Scores: bonds: 0.51 angles: 1.19 torsions: N/A planes: 1.81 non-bonded: 0.01 chiral vol: 0.99 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.83 Refinement elapsed time: 0.18 refinement results: ['', 0, [['Bonds', 'Bonds: 0.510', 0.5100934505462646], ['Angles', 'Angles: 1.188', 1.188403844833374], ['Planes', 'Planes: 1.809', 1.8088258504867554], ['Non-bonded', 'Non-bonded: 0.095', 0.09466713666915894], ['Chirals', 'Chirals: 0.992', 0.9923803210258484]]] :::: ow factor 1.12492586672 INFO:: setting refinement weight to 5.02534535027 from 6.35936450958 / ( 1.12492586672 * 1.12492586672 ) ---------------------------------------------- ---------------------------------------------- ERROR:: A: last_restraints no cleared up ---------------------------------------------- ---------------------------------------------- INFO:: created 67 restraints created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 3.36 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 FAIL close enough with closer than dist_crit 5.91 Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 868 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 6793.92 Initial RMS Z values bonds: 0.94 angles: 1.06 torsions: N/A planes: 1.98 non-bonded: 7.48 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 9) at -810.81 Final Estimated RMS Z Scores: bonds: 0.45 angles: 1.13 torsions: N/A planes: 1.79 non-bonded: 0.01 chiral vol: 0.93 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.05 Refinement elapsed time: 0.22 refinement results: ['', 0, [['Bonds', 'Bonds: 0.454', 0.45446667075157166], ['Angles', 'Angles: 1.126', 1.1264508962631226], ['Planes', 'Planes: 1.795', 1.7946611642837524], ['Non-bonded', 'Non-bonded: 0.085', 0.0851701945066452], ['Chirals', 'Chirals: 0.935', 0.9346172213554382]]] :::: ow factor 1.07754898816 ok test20_2 (__main__.PdbMtzTestFunctions) Neighbour-Refine doesn't destroy disulfide bonds ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 34 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (set-go-to-atom-molecule 34) ---------------------------------------------- ---------------------------------------------- ERROR:: A: last_restraints no cleared up ---------------------------------------------- ---------------------------------------------- INFO:: created 41 restraints created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints FAIL close enough with closer than dist_crit 3.44 FAIL close enough with closer than dist_crit 3.44 FAIL close enough with closer than dist_crit 3.44 FAIL close enough with closer than dist_crit 3.44 FAIL close enough with closer than dist_crit 5.07 FAIL close enough with closer than dist_crit 5.07 FAIL close enough with closer than dist_crit 5.07 FAIL close enough with closer than dist_crit 5.07 FAIL close enough with closer than dist_crit 3.28 FAIL close enough with closer than dist_crit 3.28 FAIL close enough with closer than dist_crit 3.28 FAIL close enough with closer than dist_crit 3.28 Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 6 bond links 17 angle links 10 plane links 5 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 632 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -723.53 Initial RMS Z values bonds: 1.64 angles: 1.05 torsions: N/A planes: 0.74 non-bonded: 0.03 chiral vol: 0.51 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -842.90 Final Estimated RMS Z Scores: bonds: 0.29 angles: 0.69 torsions: N/A planes: 0.66 non-bonded: 0.01 chiral vol: 0.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.10 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz INFO:: replace_coords: 21 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: created 41 restraints created 18 bond restraints created 20 angle restraints created 0 plane restraints created 3 chiral vol restraints FAIL close enough with closer than dist_crit 3.32 FAIL close enough with closer than dist_crit 3.32 FAIL close enough with closer than dist_crit 3.32 FAIL close enough with closer than dist_crit 3.32 FAIL close enough with closer than dist_crit 5.08 FAIL close enough with closer than dist_crit 5.08 FAIL close enough with closer than dist_crit 5.08 FAIL close enough with closer than dist_crit 5.08 FAIL close enough with closer than dist_crit 3.33 FAIL close enough with closer than dist_crit 3.33 FAIL close enough with closer than dist_crit 3.33 FAIL close enough with closer than dist_crit 3.33 Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 6 bond links 17 angle links 10 plane links 5 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 631 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -842.90 Initial RMS Z values bonds: 0.29 angles: 0.69 torsions: N/A planes: 0.66 non-bonded: 0.01 chiral vol: 0.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -842.90 Final Estimated RMS Z Scores: bonds: 0.29 angles: 0.69 torsions: N/A planes: 0.65 non-bonded: 0.01 chiral vol: 0.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.12 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:15_2018_modification_1.pdb.gz INFO:: replace_coords: 21 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/alt-conf-waters.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-waters.pdb PDB file /home/paule/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 35 read successfully DEBUG:: there were 0 types with no dictionary masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-waters.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... INFO:: Command: (update-go-to-atom-window-on-other-molecule-chosen) INFO:: Command: (set-go-to-atom-molecule 0) INFO:: Command: (set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B") ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/backrub-fragment.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/backrub-fragment.pdb PDB file /home/paule/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (copy-molecule 36) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Wed_Sep_19_11:45:15_2018_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "/RNASE3GMP/COMPLEX/FWT" "/RNASE3GMP/COMPLEX/PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/test-TER-OXT.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/test-TER-OXT.pdb PDB file /home/paule/data/greg-data/test-TER-OXT.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 39 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_test-TER-OXT.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.13,-9.09,14.92) B-factor: 45.00 INFO:: Command: (add-OXT-to-residue 39 14 "" "A") debug:: add_OXT_to_residue() returns istat 1 WARNING:: This residue already has an OXT - aborting INFO:: Command: (add-OXT-to-residue 39 14 "" "A") debug:: add_OXT_to_residue() returns istat 0 INFO:: Command: (write-pdb-file 39 "test-TER-OXT-added.pdb") found TER TER 25 ASP A 14 ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/val.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/val.pdb PDB file /home/paule/data/greg-data/val.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 40 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_home_paule_data_greg-data_val.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz INFO:: Command: (mutate 40 "C" 3 "" "HIS") INFO:: Command: (write-pdb-file 40 "his.pdb") ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2yie-frag.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2yie-frag.pdb PDB file /home/paule/data/greg-data/2yie-frag.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 41 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_2yie-frag.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04 rms devi: 0.05 max devi: 0.08 min devi: 0.01 INFO:: Command: (mutate-base 41 "X" 54 "" "C") INFO:: Command: (write-pdb-file 41 "2yie-mutated.pdb") ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/4f8g.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 42 read successfully DEBUG:: there were 1 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04 rms devi: 0.05 max devi: 0.07 min devi: 0.01 INFO:: Command: (mutate-base 42 "A" 19 "" "DC") INFO:: Command: (write-pdb-file 42 "test-1.pdb") ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/4f8g.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 43 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Wed_Sep_19_11:45:15_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04 rms devi: 0.04 max devi: 0.07 min devi: 0.02 INFO:: Command: (mutate-base 43 "A" 10 "" "DT") INFO:: Command: (write-pdb-file 43 "test-2.pdb") ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... failed to delete residue atoms A 88 :A: INFO:: Command: (delete-residue-with-full_spec 0 1 "A" 88 "" "A") ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.20 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.03 seconds to read MTZ file INFO:: 0.03 seconds to initialize map INFO:: 0.04 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.05 Map minimum: ..... -0.92 INFO:: 0.00 seconds for contour map INFO:: 0.11 seconds in total INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 46 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.00 st.d: 0.31 Map statistics: min: -0.90, max: 2.76 -0.85 7 -0.76 47 -0.67 345 -0.58 1966 -0.48 7547 -0.39 21145 -0.30 36984 -0.21 49747 -0.12 62502 -0.03 78146 0.06 56227 0.16 31741 0.25 15372 0.34 9396 0.43 7278 0.52 6354 0.61 5287 0.71 4622 0.80 3865 0.89 3168 0.98 2366 1.07 1769 1.16 1258 1.25 879 1.35 637 1.44 417 1.53 237 1.62 135 1.71 69 1.80 46 1.89 18 1.99 8 2.08 2 2.17 6 2.26 2 2.35 0 2.44 1 2.54 3 2.63 0 2.72 1 2.81 0 INFO:: Command: (atom_info_string 46 A 20 CA ) INFO:: Command: (atom_info_string 46 A 21 CA ) INFO:: Command: (atom_info_string 46 A 22 CA ) INFO:: Command: (atom_info_string 46 A 23 CA ) INFO:: Command: (atom_info_string 46 A 24 CA ) INFO:: Command: (atom_info_string 46 A 25 CA ) INFO:: Command: (atom_info_string 46 A 26 CA ) INFO:: Command: (atom_info_string 46 A 27 CA ) INFO:: Command: (atom_info_string 46 A 28 CA ) INFO:: Command: (atom_info_string 46 A 29 CA ) INFO:: Command: (atom_info_string 46 A 30 CA ) INFO:: Command: (atom_info_string 46 A 1 CA ) INFO:: Command: (atom_info_string 46 A 2 CA ) INFO:: Command: (atom_info_string 46 A 3 CA ) INFO:: Command: (atom_info_string 46 A 4 CA ) INFO:: Command: (atom_info_string 46 A 5 CA ) INFO:: Command: (atom_info_string 46 A 6 CA ) INFO:: Command: (atom_info_string 46 A 7 CA ) INFO:: Command: (atom_info_string 46 A 8 CA ) INFO:: Command: (atom_info_string 46 A 9 CA ) INFO:: Command: (atom_info_string 46 A 10 CA ) high-values: [0.7880393862724304, 0.9311162829399109, 0.9948475360870361, 1.0713924169540405, 0.7348382472991943, 0.8019416332244873, 0.6376815438270569, 0.6461937427520752, 0.952126145362854, 0.9289178252220154, 0.9664078950881958] low values: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] Map statistics: mean: -0.00 st.d: 0.06 Map statistics: min: -2.98, max: 0.75 -2.93 1 -2.84 1 -2.74 1 -2.65 2 -2.56 2 -2.47 0 -2.37 2 -2.28 1 -2.19 1 -2.09 4 -2.00 2 -1.91 3 -1.81 4 -1.72 4 -1.63 8 -1.53 11 -1.44 15 -1.35 33 -1.26 33 -1.16 49 -1.07 65 -0.98 120 -0.88 145 -0.79 159 -0.70 202 -0.60 249 -0.51 275 -0.42 291 -0.32 411 -0.23 440 -0.14 581 -0.05 300752 0.05 101991 0.14 1213 0.23 1098 0.33 767 0.42 463 0.51 156 0.61 36 0.70 8 0.79 1 diff-high-values: [0.0032140458934009075, 0.005670706741511822, 0.0031834905967116356, 0.0036503991577774286, 0.005187051370739937, 0.0033501957077533007, 0.0024679440539330244, 0.007025451865047216, 0.004253388848155737, -0.0006197448819875717, 0.0035091182217001915] diff-low-values: [-0.5327256321907043, -0.9398592710494995, -0.7048763632774353, -0.827702522277832, -0.8482539653778076, -1.0417752265930176, -1.1633360385894775, -1.1859604120254517, -0.8826918005943298, -0.8691443204879761] ok test29_1 (__main__.PdbMtzTestFunctions) Skeletonize a map ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 49 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: Command: (close-molecule 49) INFO:: Command: (close-molecule 50) ok test29_2 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.80 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.01 Map minimum: ..... -0.90 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.50 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.03 seconds to read MTZ file INFO:: 0.04 seconds to initialize map INFO:: 0.05 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.07 Map minimum: ..... -0.88 INFO:: 0.00 seconds for contour map INFO:: 0.14 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 128, 160, 80) by 1.00 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1.00 Map statistics: mean: 0.00 st.d: 0.31 Map statistics: min: -0.89, max: 3.01 -0.85 8 -0.75 64 -0.65 542 -0.55 3067 -0.46 12045 -0.36 29986 -0.26 46658 -0.16 61563 -0.07 73639 0.03 68489 0.13 41912 0.23 19494 0.33 11050 0.42 8221 0.52 7074 0.62 5839 0.72 5071 0.81 4183 0.91 3295 1.01 2384 1.11 1722 1.20 1175 1.30 843 1.40 560 1.50 325 1.59 179 1.69 90 1.79 59 1.89 23 1.98 9 2.08 8 2.18 6 2.28 2 2.37 2 2.47 4 2.57 3 2.67 2 2.76 2 2.86 1 2.96 0 3.06 1 Map statistics: mean: -0.00 st.d: 0.00 Map statistics: min: -0.01, max: 0.01 -0.01 1 -0.01 1 -0.01 0 -0.01 1 -0.01 3 -0.01 2 -0.01 4 -0.01 7 -0.01 25 -0.01 37 -0.01 103 -0.00 260 -0.00 640 -0.00 1269 -0.00 2611 -0.00 5434 -0.00 10529 -0.00 21799 -0.00 51978 -0.00 109495 0.00 110465 0.00 52013 0.00 20447 0.00 9606 0.00 5236 0.00 2974 0.00 1857 0.00 1167 0.00 683 0.01 388 0.01 223 0.01 139 0.01 86 0.01 56 0.01 25 0.01 16 0.01 7 0.01 4 0.01 4 0.01 4 0.01 1 INFO:: map sigmas: normal 0.311081498861 and diff-map: 0.00107625476085 ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/multi-carbo-coot-3.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/multi-carbo-coot-3.pdb PDB file /home/paule/data/greg-data/multi-carbo-coot-3.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 55 read successfully DEBUG:: there were 2 types with no dictionary bond-length: 2.2472994905 INFO:: created 138 restraints created 46 bond restraints created 82 angle restraints created 2 plane restraints created 8 chiral vol restraints DEBUG:: find_link_type_complicado() find_glycosidic_linkage_type() returns "ALPHA1-4" Link restraints: 1 bond links 3 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 799 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2651.72 Initial RMS Z values bonds: 6.16 angles: 2.85 torsions: N/A planes: 0.08 non-bonded: 0.21 chiral vol: 0.90 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 887) at 15.99 Final Estimated RMS Z Scores: bonds: 0.10 angles: 0.42 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: 0.16 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.63 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-3.pdb_Wed_Sep_19_11:45:16_2018_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it bond-length: 1.44437913592 ok test30_1 (__main__.PdbMtzTestFunctions) Refine an NAG-ASN Link ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb PDB file /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 3 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 4/110 Molecule 56 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.50 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.03 seconds to read MTZ file INFO:: 0.01 seconds to initialize map INFO:: 0.02 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 2.98 Map minimum: ..... -0.88 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total ......... checking for /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab ..that failed - trying /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/NAG-decorations.tab INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:45:16_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:45:16_2018_modification_1.pdb.gz INFO:: link torsion generated from link bond restraint INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:45:16_2018_modification_2.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 698 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 66613.86 Initial RMS Z values bonds: 0.36 angles: 0.61 torsions: N/A planes: 0.68 non-bonded: 95.81 chiral vol: 0.44 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 44) at -147.35 Final Estimated RMS Z Scores: bonds: 2.00 angles: 1.38 torsions: N/A planes: 0.99 non-bonded: 0.06 chiral vol: 0.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.43 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:45:16_2018_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: link torsion generated from link bond restraint INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:45:16_2018_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 651 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 20405.31 Initial RMS Z values bonds: 2.00 angles: 1.38 torsions: N/A planes: 0.99 non-bonded: 31.64 chiral vol: 0.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 127) at -139.96 Final Estimated RMS Z Scores: bonds: 1.87 angles: 1.42 torsions: N/A planes: 0.84 non-bonded: 0.06 chiral vol: 0.87 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.04 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:45:16_2018_modification_5.pdb.gz INFO:: replace_coords: 22 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 452 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 26835.39 Initial RMS Z values bonds: 1.87 angles: 1.42 torsions: N/A planes: 0.84 non-bonded: 59.77 chiral vol: 0.87 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 20) at -90.87 Final Estimated RMS Z Scores: bonds: 1.99 angles: 1.46 torsions: N/A planes: 0.87 non-bonded: 0.09 chiral vol: 0.65 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.17 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:45:16_2018_modification_6.pdb.gz INFO:: replace_coords: 22 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-VAL.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-VAL.pdb PDB file /home/paule/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 58 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 1 CB INFO:: created 40 restraints created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 44 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 5.00 Initial RMS Z values bonds: 0.54 angles: 0.16 torsions: N/A planes: N/A non-bonded: 0.00 chiral vol: 0.45 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.25 Final Estimated RMS Z Scores: bonds: 0.01 angles: 0.09 torsions: N/A planes: N/A non-bonded: 0.00 chiral vol: 0.15 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.24 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: undo molecule number set to: 58 INFO:: Command: (set-undo-molecule 58) INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:45:18_2018_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 INFO:: Command: (apply-undo) INFO:: created 40 restraints created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 44 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 5.00 Initial RMS Z values bonds: 0.54 angles: 0.16 torsions: N/A planes: N/A non-bonded: 0.00 chiral vol: 0.45 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.25 Final Estimated RMS Z Scores: bonds: 0.01 angles: 0.09 torsions: N/A planes: N/A non-bonded: 0.00 chiral vol: 0.15 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.31 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ok test32_0 (__main__.PdbMtzTestFunctions) Test for regularization and mangling of hydrogen names from a PDB v 3.0 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 59 read successfully DEBUG:: there were 0 types with no dictionary INFO:: created 49 restraints created 17 bond restraints created 31 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 67 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 903.06 Initial RMS Z values bonds: 5.62 angles: 3.43 torsions: N/A planes: N/A non-bonded: 0.00 chiral vol: 0.75 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 165) at 0.47 Final Estimated RMS Z Scores: bonds: 0.01 angles: 0.12 torsions: N/A planes: N/A non-bonded: 0.00 chiral vol: 0.14 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.36 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 0 ([['HD11', ''], [1.0, 10.53, ' H', ''], [-10.115661686805757, 6.520595083825253, 7.014073049321203], 12], [[' CD1', ''], [1.0, 11.52, ' C', ''], [-10.12800793584828, 5.646514384138953, 6.617313187656927], 6]) 1 ([['HD12', ''], [1.0, 10.13, ' H', ''], [-9.759875937014511, 5.683416692575041, 5.731440598329556], 13], [[' CD1', ''], [1.0, 11.52, ' C', ''], [-10.12800793584828, 5.646514384138953, 6.617313187656927], 6]) 2 ([['HD13', ''], [1.0, 10.56, ' H', ''], [-11.027907750618084, 5.313904338042881, 6.584925374786836], 14], [[' CD1', ''], [1.0, 11.52, ' C', ''], [-10.12800793584828, 5.646514384138953, 6.617313187656927], 6]) 3 ([['HD21', ''], [1.0, 10.15, ' H', ''], [-7.993943443152581, 3.1528858672455002, 7.144379675781024], 15], [[' CD2', ''], [1.0, 11.96, ' C', ''], [-8.558966269319, 3.696134732079038, 6.590104923429545], 7]) 4 ([['HD22', ''], [1.0, 10.3, ' H', ''], [-9.20783231834719, 3.1465252844449627, 6.14453380682276], 16], [[' CD2', ''], [1.0, 11.96, ' C', ''], [-8.558966269319, 3.696134732079038, 6.590104923429545], 7]) 5 ([['HD23', ''], [1.0, 10.65, ' H', ''], [-8.028463147863336, 4.16698137417791, 5.943364044877233], 17], [[' CD2', ''], [1.0, 11.96, ' C', ''], [-8.558966269319, 3.696134732079038, 6.590104923429545], 7]) ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... looping over restraint plane restraint: [plane-restraint: plan {12 atoms} : CB 0.02: : CG 0.02: : CD1 0.02: : CE1 0.02: : CZ 0.02: : CE2 0.02: : CD2 0.02: : OH 0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ] INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: created 28 restraints created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 40 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2866.94 Initial RMS Z values bonds: 1.15 angles: 0.85 torsions: N/A planes: 3.06 non-bonded: 79.86 chiral vol: 0.76 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 17) at -327.94 Final Estimated RMS Z Scores: bonds: 0.27 angles: 0.21 torsions: N/A planes: 0.22 non-bonded: 0.01 chiral vol: 0.08 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.40 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Bond-length: 2.62831301549 pass intermediate 2.8 tolerance test looping over restraint plane restraint: [plane-restraint: plan {12 atoms} : CB 0.02: : CG 0.02: : CD1 0.02: : CE1 0.02: : CZ 0.02: : CE2 0.02: : CD2 0.02: : OH 0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ] INFO:: created 29 restraints created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 39 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2246.42 Initial RMS Z values bonds: 14.65 angles: 0.21 torsions: N/A planes: 0.22 non-bonded: 0.00 chiral vol: 0.08 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 134) at -361.45 Final Estimated RMS Z Scores: bonds: 0.09 angles: 0.11 torsions: N/A planes: 0.28 non-bonded: 0.00 chiral vol: 0.02 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.43 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it OK plane atom CB Bond-length: 1.5143884733 ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... INFO:: wrote mmCIF "coot-test-ala.cif" ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-ACT.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 61 read successfully DEBUG:: there were 1 types with no dictionary Welcome to Coot looping over restraint plane restraint: [plane-restraint: plan-1 {4 atoms} : C 0.02: : O 0.02: : OXT 0.02: : CH3 0.02: ] INFO:: created 15 restraints created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 7 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 4835.20 Initial RMS Z values bonds: 0.01 angles: 0.01 torsions: N/A planes: 0.00 non-bonded: 689.93 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 96) at -88.85 Final Estimated RMS Z Scores: bonds: 0.02 angles: 0.11 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.60 Refinement elapsed time: 0.02 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 62 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_2.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_3.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_6.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_7.pdb.gz INFO:: Command: (n-chains 62) INFO:: Command: (chain_id 62 0) INFO:: Command: (chain_id 62 1) INFO:: Command: (chain_id 62 2) INFO:: Command: (chain_id 62 3) INFO:: Command: (chain_id 62 4) INFO:: Command: (chain_id 62 5) INFO:: Command: (chain_id 62 6) INFO:: Command: (chain_id 62 7) INFO:: Command: (chain_id 62 8) ok test35_1 (__main__.PdbMtzTestFunctions) Chain-ids in links change also on change chain id ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 63 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz FAIL close enough with closer than dist_crit 25.37 FAIL close enough with closer than dist_crit 25.37 FAIL close enough with closer than dist_crit 25.37 FAIL close enough with closer than dist_crit 25.37 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_1.pdb.gz ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... INFO:: Command: (copy-molecule 0) INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.76) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.18 rms devi: 4.86 max devi: 46.26 min devi: 0.13 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:: Command: (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Command: (replace-fragement 64 65 "//A70-80") distances: [20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966] ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... found 6 neighbours [['A', 39, ''], ['A', 41, ''], ['A', 38, ''], ['B', 61, ''], ['A', 42, ''], ['B', 60, '']] found 0 neighbours [] ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:18_2018_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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:: Command: (turn-off-backup 67) INFO:: Command: (rotamer-score 67 "A" 28 "") Rotamer 0 : m-85 100.0 INFO:: Command: (rotamer-score 67 "A" 28 "") Rotamer 1 : t80 90.1668395996 INFO:: Command: (rotamer-score 67 "A" 28 "") Rotamer 2 : p90 50.7077865601 INFO:: Command: (rotamer-score 67 "A" 28 "") Rotamer 3 : m -30 21.4231548309 INFO:: Command: (rotamer-score 67 "A" 28 "") Rotamer 4 : m -30 21.4231548309 INFO:: Command: (turn-on-backup 67) ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/paule/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 in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 50/87 Molecule 68 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 68 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -3.00 is_nucleic_acid_flag 0 console_output 1 --------------------------------------------------- INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb > target sequence: ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID ||||||| |||||||||| ||||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| DVSGTVCLSALPPEATDTLNLIAS-DGPFPYSQ-DGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 150.00 DEBUG:: s.length() 95 DEBUG:: nSelResidues 87 INFO:: backup file coot-backup/_home_paule_data_greg-data_rnase-A-needs-an-insertion.pdb_Wed_Sep_19_11:45:19_2018_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: 212312408 "A" 1 ""] -> ASP [spec: 212312408 "A" 2 ""] -> VAL [spec: 212312408 "A" 3 ""] -> SER [spec: 212312408 "A" 11 ""] -> LEU [spec: 212312408 "A" 12 ""] -> PRO [spec: 212312408 "A" 13 ""] -> PRO [spec: 147771224 "A" 62 ""] -> PRO [spec: 147771224 "A" 63 ""] -> GLY Deletions: [spec: 147771224 "A" 25 ""] [spec: 147771224 "A" 34 ""] Mutations: [spec: 147771224 "A" 24 ""] -> SER [spec: 147771224 "A" 33 ""] -> GLN INFO:: mutate 24 A to a SER INFO:: mutate 33 A to a GLN apply resno updates... Applied 3 insertions Applied 2 mutations Applied 2 deletions INFO:: Command: (write-pdb-file 68 "mutated.pdb") ::::: [68, 'A', 1, ''] ::::: [68, 'A', 4, ''] ::::: [68, 'A', 59, ''] ::::: [68, 'A', 60, ''] ::::: [68, 'A', 61, ''] ::::: [68, 'A', 93, ''] ::::: [68, 'A', 94, ''] results [True, True, True, True, True, True, True] ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 69 "A" 10 20 100) INFO:: Command: (seqnum-from-serial-number 69 "A" 90) INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 70 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 70 "A" 10 20 -100) INFO:: Command: (seqnum-from-serial-number 70 "A" 0) ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb3hfl.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3hfl.ent PDB file /home/paule/data/greg-data/pdb3hfl.ent has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 71 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.50 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.03 seconds to read MTZ file INFO:: 0.01 seconds to initialize map INFO:: 0.01 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.26 Map maximum: ..... 1.72 Map minimum: ..... -1.03 INFO:: 0.00 seconds for contour map INFO:: 0.05 seconds in total INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.83 INFO:: Command: (auto-fit-best-rotamer 52 "" "A" "H" 71 72 0 0.00) INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Wed_Sep_19_11:45:19_2018_modification_1.pdb.gz ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Sep_19_11:45:19_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.55 min devi: 0.08 INFO:: Command: (mutate-base 73 "A" 2 "" "C") mutated base to type C - was A INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Sep_19_11:45:19_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.55 min devi: 0.08 INFO:: Command: (mutate-base 74 "A" 2 "" "Cr") mutated base to type Cr - was A ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.09 INFO:: Command: (mutate-base 75 "A" 2 "" "DC") mutated base to type DC INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: Command: (mutate-base 75 "A" 2 "" "DG") mutated base to type DG INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.01 min devi: 0.00 INFO:: Command: (mutate-base 75 "A" 2 "" "DA") mutated base to type DA INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.50 min devi: 0.09 INFO:: Command: (mutate-base 75 "A" 2 "" "DT") mutated base to type DT INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.01 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.51 min devi: 0.10 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.09 INFO:: Command: (mutate-base 76 "A" 2 "" "Cd") mutated base to type Cd INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.53 min devi: 0.09 INFO:: Command: (mutate-base 76 "A" 2 "" "Gd") mutated base to type Gd INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.01 min devi: 0.00 INFO:: Command: (mutate-base 76 "A" 2 "" "Ad") mutated base to type Ad INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:45:19_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.50 min devi: 0.09 INFO:: Command: (mutate-base 76 "A" 2 "" "Td") mutated base to type Td ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... INFO:: Command: (copy-molecule 0) INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Command: (mutate 77 "A" 32 "" "LYS") ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/some-waters-with-ter.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/some-waters-with-ter.pdb PDB file /home/paule/data/greg-data/some-waters-with-ter.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 78 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (set-rotation-centre 3.00 4.00 5.00) INFO:: backup file coot-backup/_home_paule_data_greg-data_some-waters-with-ter.pdb_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3.00,4.00,5.00) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (write-pdb-file 78 "tmp-with-new-water.pdb") ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tm+some-waters.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tm+some-waters.pdb PDB file /home/paule/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 79 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 0.20 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.31 INFO:: Using density cut-off: 0.06 (0.20 sigma) (mean -0.03 stdev: 0.15) INFO:: Blobs with volume larger than 11.00 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.40 3.20 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 27.82, 31.44, 8.887) is too big to be water INFO:: cluster at xyz = ( 70.04, 19.1, 18.63) is too big to be water INFO:: cluster at xyz = ( 69.25, 5.345, 11.11) is too big to be water INFO:: cluster at xyz = ( 52.69, 10.79, 11.51) is too big to be water INFO:: cluster at xyz = ( 72.02, 12.27, 14.68) is too big to be water INFO:: cluster at xyz = ( 39.69, 8.165, 19.55) is too big to be water INFO:: cluster at xyz = ( 53.3, -4.968, -2.722) is too big to be water INFO:: cluster at xyz = ( 40.99, 7.049, 16.27) is too big to be water INFO:: cluster at xyz = ( 25.71, 4.246, 5.745) is too big to be water INFO:: found 46 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_tm+some-waters.pdb_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Command: (write-pdb-file 79 "auto-waters.pdb") ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:19_2018_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/water-test-no-cell.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/water-test-no-cell.pdb PDB file /home/paule/data/greg-data/water-test-no-cell.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 81 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_water-test-no-cell.pdb_Wed_Sep_19_11:45:22_2018_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pathological-water-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pathological-water-test.pdb PDB file /home/paule/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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_paule_data_greg-data_pathological-water-test.pdb_Wed_Sep_19_11:45:22_2018_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: Command: (write-pdb-file 82 "waters-moved-failure.pdb") ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... INFO:: Command: (copy-molecule 0) INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.50 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.02 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 2.98 Map minimum: ..... -0.88 INFO:: 0.00 seconds for contour map INFO:: 0.05 seconds in total fitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:22_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:22_2018_modification_1.pdb.gz INFO:: Command: (add-terminal-residue 83 "A" 93 1) ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... INFO:: Command: (copy-molecule 0) INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.76) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.18 rms devi: 4.86 max devi: 46.26 min devi: 0.13 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" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 85 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 85 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.76) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.18 rms devi: 4.86 max devi: 46.26 min devi: 0.13 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) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:22_2018_modification_0.pdb.gz ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 86 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (turn-off-backup 86) 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.60,8.69,12.91) B-factor: 45.00 added to molecule (and new chain) INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 43.60 8.69 12.91) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 45.60 8.69 12.91) 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 47.60 8.69 12.91) 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 49.60 8.69 12.91) 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 51.60 8.69 12.91) INFO:: Command: (renumber-residue-range 86 "D" 1 5 10) 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 53.60 8.69 12.91) 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 55.60 8.69 12.91) 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 57.60 8.69 12.91) 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 59.60 8.69 12.91) 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 61.60 8.69 12.91) INFO:: Command: (renumber-residue-range 86 "E" 11 15 5) 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 63.60 8.69 12.91) 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 65.60 8.69 12.91) 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 67.60 8.69 12.91) 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 69.60 8.69 12.91) 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.60,8.69,12.91) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 71.60 8.69 12.91) INFO:: Command: (renumber-residue-range 86 "F" 16 20 2) INFO:: Command: (n-chains 86) INFO:: Command: (chain_id 86 0) INFO:: Command: (chain_id 86 1) INFO:: Command: (chain_id 86 2) INFO:: Command: (chain_id 86 3) INFO:: Command: (chain_id 86 4) INFO:: Command: (is-solvent-chain-p 86 "A") INFO:: Command: (is-solvent-chain-p 86 "B") INFO:: Command: (is-solvent-chain-p 86 "D") INFO:: Command: (is-solvent-chain-p 86 "E") INFO:: Command: (is-solvent-chain-p 86 "F") INFO:: Command: (resname-from-serial-number 86 "D" 0) INFO:: Command: (seqnum-from-serial-number 86 "D" 0) INFO:: Command: (insertion-code-from-serial-number 86 "D" 0) INFO:: Command: (resname-from-serial-number 86 "D" 1) INFO:: Command: (seqnum-from-serial-number 86 "D" 1) INFO:: Command: (insertion-code-from-serial-number 86 "D" 1) INFO:: Command: (resname-from-serial-number 86 "D" 2) INFO:: Command: (seqnum-from-serial-number 86 "D" 2) INFO:: Command: (insertion-code-from-serial-number 86 "D" 2) INFO:: Command: (resname-from-serial-number 86 "D" 3) INFO:: Command: (seqnum-from-serial-number 86 "D" 3) INFO:: Command: (insertion-code-from-serial-number 86 "D" 3) INFO:: Command: (resname-from-serial-number 86 "D" 4) INFO:: Command: (seqnum-from-serial-number 86 "D" 4) INFO:: Command: (insertion-code-from-serial-number 86 "D" 4) INFO:: Command: (does-residue-exist-p 86 D 1 ) INFO:: Command: (does-residue-exist-p 86 D 2 ) INFO:: Command: (does-residue-exist-p 86 D 3 ) INFO:: Command: (does-residue-exist-p 86 D 4 ) INFO:: Command: (does-residue-exist-p 86 D 5 ) INFO:: Command: (resname-from-serial-number 86 "E" 0) INFO:: Command: (seqnum-from-serial-number 86 "E" 0) INFO:: Command: (insertion-code-from-serial-number 86 "E" 0) INFO:: Command: (resname-from-serial-number 86 "E" 1) INFO:: Command: (seqnum-from-serial-number 86 "E" 1) INFO:: Command: (insertion-code-from-serial-number 86 "E" 1) INFO:: Command: (resname-from-serial-number 86 "E" 2) INFO:: Command: (seqnum-from-serial-number 86 "E" 2) INFO:: Command: (insertion-code-from-serial-number 86 "E" 2) INFO:: Command: (resname-from-serial-number 86 "E" 3) INFO:: Command: (seqnum-from-serial-number 86 "E" 3) INFO:: Command: (insertion-code-from-serial-number 86 "E" 3) INFO:: Command: (resname-from-serial-number 86 "E" 4) INFO:: Command: (seqnum-from-serial-number 86 "E" 4) INFO:: Command: (insertion-code-from-serial-number 86 "E" 4) INFO:: Command: (does-residue-exist-p 86 E 1 ) INFO:: Command: (does-residue-exist-p 86 E 2 ) INFO:: Command: (does-residue-exist-p 86 E 3 ) INFO:: Command: (does-residue-exist-p 86 E 4 ) INFO:: Command: (does-residue-exist-p 86 E 5 ) INFO:: Command: (resname-from-serial-number 86 "F" 0) INFO:: Command: (seqnum-from-serial-number 86 "F" 0) INFO:: Command: (insertion-code-from-serial-number 86 "F" 0) INFO:: Command: (resname-from-serial-number 86 "F" 1) INFO:: Command: (seqnum-from-serial-number 86 "F" 1) INFO:: Command: (insertion-code-from-serial-number 86 "F" 1) INFO:: Command: (resname-from-serial-number 86 "F" 2) INFO:: Command: (seqnum-from-serial-number 86 "F" 2) INFO:: Command: (insertion-code-from-serial-number 86 "F" 2) INFO:: Command: (resname-from-serial-number 86 "F" 3) INFO:: Command: (seqnum-from-serial-number 86 "F" 3) INFO:: Command: (insertion-code-from-serial-number 86 "F" 3) INFO:: Command: (resname-from-serial-number 86 "F" 4) INFO:: Command: (seqnum-from-serial-number 86 "F" 4) INFO:: Command: (insertion-code-from-serial-number 86 "F" 4) INFO:: Command: (does-residue-exist-p 86 F 1 ) INFO:: Command: (does-residue-exist-p 86 F 2 ) INFO:: Command: (does-residue-exist-p 86 F 3 ) INFO:: Command: (does-residue-exist-p 86 F 4 ) INFO:: Command: (does-residue-exist-p 86 F 5 ) INFO:: Command: (renumber-residue-range 86 "E" 1 5 5) INFO:: Command: (renumber-residue-range 86 "F" 1 5 10) INFO:: Command: (turn-on-backup 86) INFO:: Command: (n-chains 86) INFO:: Command: (chain_id 86 2) INFO:: Command: (seqnum-from-serial-number 86 "D" 0) INFO:: Command: (seqnum-from-serial-number 86 "D" 14) ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices 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 87 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-ACT.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 88 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-NPO.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 89 read successfully DEBUG:: there were 1 types with no dictionary -------- starting chain list ----------- INFO:: Command: (n-chains 87) INFO:: Command: (chain_id 87 0) INFO:: Command: (chain_id 87 1) INFO:: Command: (chain_id 87 2) INFO:: Command: (chain_id 87 3) INFO:: Command: (chain_id 87 4) ['A', 'B', 'C', 'D', ''] -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0.00 0.00 0.33 pre-trans: 0 0 0 INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.57,-20.50,95.47) B-factor: 45.26 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (64.42,-37.85,121.39) B-factor: 88.52 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.50 rms devi: 2.80 max devi: 6.69 min devi: 0.44 find_ncs_matrix returns (LSQ) | 0.8045, 0.069, 0.59| | 0.5435, 0.315, -0.778| | -0.2395, 0.9466, 0.2159| ( -57.32, 43.57, 131.4) INFO:: NCS chain comparison 66/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.57,-20.50,95.47) B-factor: 45.26 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (-18.26,-63.04,111.43) B-factor: 50.76 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.97 rms devi: 2.17 max devi: 4.54 min devi: 0.43 find_ncs_matrix returns (LSQ) | -0.5596, -0.8266, 0.06065| | -0.8239, 0.5468, -0.1492| | 0.09015, -0.1334, -0.9869| ( -4.436, 16.92, 204.3) INFO:: NCS chain comparison 61/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.57,-20.50,95.47) B-factor: 45.26 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (-0.29,-72.48,94.47) B-factor: 78.35 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.70 rms devi: 4.09 max devi: 9.44 min devi: 0.29 find_ncs_matrix returns (LSQ) | -0.4782, -0.7381, -0.476| | -0.7473, 0.05733, 0.662| | -0.4613, 0.6723, -0.579| ( 53.45, -87.51, 210.2) INFO:: NCS chain comparison 0/67 INFO:: NCS chain comparison 0/67 INFO:: NCS chain comparison 0/54 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:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (n-chains 87) INFO:: Command: (chain_id 87 0) INFO:: Command: (chain_id 87 1) INFO:: Command: (chain_id 87 2) INFO:: Command: (chain_id 87 3) INFO:: Command: (chain_id 87 4) INFO:: Command: (chain_id 87 5) INFO:: Command: (chain_id 87 6) INFO:: Command: (chain_id 87 7) INFO:: Command: (chain_id 87 8) INFO:: Command: (chain_id 87 9) INFO:: Command: (chain_id 87 10) INFO:: Command: (chain_id 87 11) ['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K'] INFO:: Command: (write-pdb-file 87 "sym-merged.pdb") ok test52_2 (__main__.PdbMtzTestFunctions) Test for good chain ids after a merge ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 91 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_0.pdb.gz INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_0.pdb.gz INFO:: Command: (n-chains 91) INFO:: Command: (chain_id 91 0) INFO:: Command: (chain_id 91 1) INFO:: Command: (chain_id 91 2) chain_ids ['AAA', 'B', 'B-chain'] INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_1.pdb.gz INFO:: Command: (n-chains 91) INFO:: Command: (chain_id 91 0) INFO:: Command: (chain_id 91 1) INFO:: Command: (chain_id 91 2) INFO:: Command: (chain_id 91 3) --- chain-ids: ['AAA', 'B', 'B-chain', 'AAA_2'] ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... INFO:: Command: (copy-molecule 0) INFO:: Command: (copy-molecule 0) INFO:: Matching/moving molecule number 94 to 93 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.04 rms devi: 0.04 max devi: 0.05 min devi: 0.02 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_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 95 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1py3.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices 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 96 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: spacegroup: P 21 21 21 INFO:: spacegroup: C 1 2 1 INFO:: Matching/moving molecule number 95 to 96 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.50 rms devi: 0.59 max devi: 1.68 min devi: 0.04 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_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 97 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_0.pdb.gz INFO:: Command: (set-residue-name 97 "A" 37 "" "FRE") INFO:: Command: (n-chains 97) INFO:: Command: (chain_id 97 0) INFO:: Command: (chain_id 97 1) INFO:: Command: (seqnum-from-serial-number 97 "A" 0) INFO:: Command: (insertion-code-from-serial-number 97 "A" 0) INFO:: Command: (seqnum-from-serial-number 97 "A" 1) INFO:: Command: (insertion-code-from-serial-number 97 "A" 1) INFO:: Command: (seqnum-from-serial-number 97 "A" 2) INFO:: Command: (insertion-code-from-serial-number 97 "A" 2) INFO:: Command: (seqnum-from-serial-number 97 "A" 3) INFO:: Command: (insertion-code-from-serial-number 97 "A" 3) INFO:: Command: (seqnum-from-serial-number 97 "A" 4) INFO:: Command: (insertion-code-from-serial-number 97 "A" 4) INFO:: Command: (seqnum-from-serial-number 97 "A" 5) INFO:: Command: (insertion-code-from-serial-number 97 "A" 5) INFO:: Command: (seqnum-from-serial-number 97 "A" 6) INFO:: Command: (insertion-code-from-serial-number 97 "A" 6) INFO:: Command: (seqnum-from-serial-number 97 "A" 7) INFO:: Command: (insertion-code-from-serial-number 97 "A" 7) INFO:: Command: (seqnum-from-serial-number 97 "A" 8) INFO:: Command: (insertion-code-from-serial-number 97 "A" 8) INFO:: Command: (seqnum-from-serial-number 97 "A" 9) INFO:: Command: (insertion-code-from-serial-number 97 "A" 9) INFO:: Command: (seqnum-from-serial-number 97 "A" 10) INFO:: Command: (insertion-code-from-serial-number 97 "A" 10) INFO:: Command: (seqnum-from-serial-number 97 "A" 11) INFO:: Command: (insertion-code-from-serial-number 97 "A" 11) INFO:: Command: 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(insertion-code-from-serial-number 97 "B" 61) INFO:: Command: (seqnum-from-serial-number 97 "B" 62) INFO:: Command: (insertion-code-from-serial-number 97 "B" 62) INFO:: Command: (seqnum-from-serial-number 97 "B" 63) INFO:: Command: (insertion-code-from-serial-number 97 "B" 63) INFO:: Command: (seqnum-from-serial-number 97 "B" 64) INFO:: Command: (insertion-code-from-serial-number 97 "B" 64) INFO:: Command: (seqnum-from-serial-number 97 "B" 65) INFO:: Command: (insertion-code-from-serial-number 97 "B" 65) INFO:: Command: (seqnum-from-serial-number 97 "B" 66) INFO:: Command: (insertion-code-from-serial-number 97 "B" 66) INFO:: Command: (seqnum-from-serial-number 97 "B" 67) INFO:: Command: (insertion-code-from-serial-number 97 "B" 67) INFO:: Command: (seqnum-from-serial-number 97 "B" 68) INFO:: Command: (insertion-code-from-serial-number 97 "B" 68) INFO:: Command: (seqnum-from-serial-number 97 "B" 69) INFO:: Command: (insertion-code-from-serial-number 97 "B" 69) INFO:: Command: 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(insertion-code-from-serial-number 97 "B" 78) INFO:: Command: (seqnum-from-serial-number 97 "B" 79) INFO:: Command: (insertion-code-from-serial-number 97 "B" 79) INFO:: Command: (seqnum-from-serial-number 97 "B" 80) INFO:: Command: (insertion-code-from-serial-number 97 "B" 80) INFO:: Command: (seqnum-from-serial-number 97 "B" 81) INFO:: Command: (insertion-code-from-serial-number 97 "B" 81) INFO:: Command: (seqnum-from-serial-number 97 "B" 82) INFO:: Command: (insertion-code-from-serial-number 97 "B" 82) INFO:: Command: (seqnum-from-serial-number 97 "B" 83) INFO:: Command: (insertion-code-from-serial-number 97 "B" 83) INFO:: Command: (seqnum-from-serial-number 97 "B" 84) INFO:: Command: (insertion-code-from-serial-number 97 "B" 84) INFO:: Command: (seqnum-from-serial-number 97 "B" 85) INFO:: Command: (insertion-code-from-serial-number 97 "B" 85) INFO:: Command: (seqnum-from-serial-number 97 "B" 86) INFO:: Command: (insertion-code-from-serial-number 97 "B" 86) INFO:: Command: (seqnum-from-serial-number 97 "B" 87) INFO:: Command: (insertion-code-from-serial-number 97 "B" 87) INFO:: Command: (seqnum-from-serial-number 97 "B" 88) INFO:: Command: (insertion-code-from-serial-number 97 "B" 88) INFO:: Command: (seqnum-from-serial-number 97 "B" 89) INFO:: Command: (insertion-code-from-serial-number 97 "B" 89) INFO:: Command: (seqnum-from-serial-number 97 "B" 90) INFO:: Command: (insertion-code-from-serial-number 97 "B" 90) INFO:: Command: (seqnum-from-serial-number 97 "B" 91) INFO:: Command: (insertion-code-from-serial-number 97 "B" 91) INFO:: Command: (seqnum-from-serial-number 97 "B" 92) INFO:: Command: (insertion-code-from-serial-number 97 "B" 92) INFO:: Command: (seqnum-from-serial-number 97 "B" 93) INFO:: Command: (insertion-code-from-serial-number 97 "B" 93) INFO:: Command: (seqnum-from-serial-number 97 "B" 94) INFO:: Command: (insertion-code-from-serial-number 97 "B" 94) INFO:: Command: (seqnum-from-serial-number 97 "B" 95) INFO:: Command: (insertion-code-from-serial-number 97 "B" 95) 0 [97, 'A', 1, ''] 1 [97, 'A', 2, ''] 2 [97, 'A', 3, ''] 3 [97, 'A', 4, ''] 4 [97, 'A', 5, ''] 5 [97, 'A', 6, ''] 6 [97, 'A', 7, ''] 7 [97, 'A', 8, ''] 8 [97, 'A', 9, ''] 9 [97, 'A', 10, ''] 10 [97, 'A', 11, ''] 11 [97, 'A', 12, ''] 12 [97, 'A', 13, ''] 13 [97, 'A', 14, ''] 14 [97, 'A', 15, ''] 15 [97, 'A', 16, ''] 16 [97, 'A', 17, ''] 17 [97, 'A', 18, ''] 18 [97, 'A', 19, ''] 19 [97, 'A', 20, ''] 20 [97, 'A', 21, ''] 21 [97, 'A', 22, ''] 22 [97, 'A', 23, ''] 23 [97, 'A', 24, ''] 24 [97, 'A', 25, ''] 25 [97, 'A', 26, ''] 26 [97, 'A', 27, ''] 27 [97, 'A', 28, ''] 28 [97, 'A', 29, ''] 29 [97, 'A', 30, ''] 30 [97, 'A', 31, ''] 31 [97, 'A', 32, ''] 32 [97, 'A', 33, ''] 33 [97, 'A', 34, ''] 34 [97, 'A', 35, ''] 35 [97, 'A', 36, ''] 36 [97, 'A', 37, ''] 36 [97, 'A', 37, ''] 37 [97, 'A', 38, ''] 38 [97, 'A', 39, ''] 39 [97, 'A', 40, ''] 40 [97, 'A', 41, ''] 41 [97, 'A', 42, ''] 42 [97, 'A', 43, ''] 43 [97, 'A', 44, ''] 44 [97, 'A', 45, ''] 45 [97, 'A', 46, ''] 46 [97, 'A', 47, ''] 47 [97, 'A', 48, ''] 48 [97, 'A', 49, ''] 49 [97, 'A', 50, ''] 50 [97, 'A', 51, ''] 51 [97, 'A', 52, ''] 52 [97, 'A', 53, ''] 53 [97, 'A', 54, ''] 54 [97, 'A', 55, ''] 55 [97, 'A', 56, ''] 56 [97, 'A', 57, ''] 57 [97, 'A', 58, ''] 58 [97, 'A', 59, ''] 59 [97, 'A', 60, ''] 60 [97, 'A', 61, ''] 61 [97, 'A', 62, ''] 62 [97, 'A', 63, ''] 63 [97, 'A', 64, ''] 64 [97, 'A', 65, ''] 65 [97, 'A', 66, ''] 66 [97, 'A', 67, ''] 67 [97, 'A', 68, ''] 68 [97, 'A', 69, ''] 69 [97, 'A', 70, ''] 70 [97, 'A', 71, ''] 71 [97, 'A', 72, ''] 72 [97, 'A', 73, ''] 73 [97, 'A', 74, ''] 74 [97, 'A', 75, ''] 75 [97, 'A', 76, ''] 76 [97, 'A', 77, ''] 77 [97, 'A', 78, ''] 78 [97, 'A', 79, ''] 79 [97, 'A', 80, ''] 80 [97, 'A', 81, ''] 81 [97, 'A', 82, ''] 82 [97, 'A', 83, ''] 83 [97, 'A', 84, ''] 84 [97, 'A', 85, ''] 85 [97, 'A', 86, ''] 86 [97, 'A', 87, ''] 87 [97, 'A', 88, ''] 88 [97, 'A', 89, ''] 89 [97, 'A', 90, ''] 90 [97, 'A', 91, ''] 91 [97, 'A', 92, ''] 92 [97, 'A', 93, ''] 93 [97, 'B', 1, ''] 94 [97, 'B', 2, ''] 95 [97, 'B', 3, ''] 96 [97, 'B', 4, ''] 97 [97, 'B', 5, ''] 98 [97, 'B', 6, ''] 99 [97, 'B', 7, ''] 100 [97, 'B', 8, ''] 101 [97, 'B', 9, ''] 102 [97, 'B', 10, ''] 103 [97, 'B', 11, ''] 104 [97, 'B', 12, ''] 105 [97, 'B', 13, ''] 106 [97, 'B', 14, ''] 107 [97, 'B', 15, ''] 108 [97, 'B', 16, ''] 109 [97, 'B', 17, ''] 110 [97, 'B', 18, ''] 111 [97, 'B', 19, ''] 112 [97, 'B', 20, ''] 113 [97, 'B', 21, ''] 114 [97, 'B', 22, ''] 115 [97, 'B', 23, ''] 116 [97, 'B', 24, ''] 117 [97, 'B', 25, ''] 118 [97, 'B', 26, ''] 119 [97, 'B', 27, ''] 120 [97, 'B', 28, ''] 121 [97, 'B', 29, ''] 122 [97, 'B', 30, ''] 123 [97, 'B', 31, ''] 124 [97, 'B', 32, ''] 125 [97, 'B', 33, ''] 126 [97, 'B', 34, ''] 127 [97, 'B', 35, ''] 128 [97, 'B', 36, ''] 129 [97, 'B', 37, ''] 130 [97, 'B', 38, ''] 131 [97, 'B', 39, ''] 132 [97, 'B', 40, ''] 133 [97, 'B', 41, ''] 134 [97, 'B', 42, ''] 135 [97, 'B', 43, ''] 136 [97, 'B', 44, ''] 137 [97, 'B', 45, ''] 138 [97, 'B', 46, ''] 139 [97, 'B', 47, ''] 140 [97, 'B', 48, ''] 141 [97, 'B', 49, ''] 142 [97, 'B', 50, ''] 143 [97, 'B', 51, ''] 144 [97, 'B', 52, ''] 145 [97, 'B', 53, ''] 146 [97, 'B', 54, ''] 147 [97, 'B', 55, ''] 148 [97, 'B', 56, ''] 149 [97, 'B', 57, ''] 150 [97, 'B', 58, ''] 151 [97, 'B', 59, ''] 152 [97, 'B', 60, ''] 153 [97, 'B', 61, ''] 154 [97, 'B', 62, ''] 155 [97, 'B', 63, ''] 156 [97, 'B', 64, ''] 157 [97, 'B', 65, ''] 158 [97, 'B', 66, ''] 159 [97, 'B', 67, ''] 160 [97, 'B', 68, ''] 161 [97, 'B', 69, ''] 162 [97, 'B', 70, ''] 163 [97, 'B', 71, ''] 164 [97, 'B', 72, ''] 165 [97, 'B', 73, ''] 166 [97, 'B', 74, ''] 167 [97, 'B', 75, ''] 168 [97, 'B', 76, ''] 169 [97, 'B', 77, ''] 170 [97, 'B', 78, ''] 171 [97, 'B', 79, ''] 172 [97, 'B', 80, ''] 173 [97, 'B', 81, ''] 174 [97, 'B', 82, ''] 175 [97, 'B', 83, ''] 176 [97, 'B', 84, ''] 177 [97, 'B', 85, ''] 178 [97, 'B', 86, ''] 179 [97, 'B', 87, ''] 180 [97, 'B', 88, ''] 181 [97, 'B', 89, ''] 182 [97, 'B', 90, ''] 183 [97, 'B', 91, ''] 184 [97, 'B', 92, ''] 185 [97, 'B', 93, ''] 186 [97, 'B', 94, ''] 187 [97, 'B', 95, ''] 188 [97, 'B', 96, ''] ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 98 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (n-chains 98) INFO:: Command: (chain_id 98 0) INFO:: Command: (chain_id 98 1) INFO:: Command: (seqnum-from-serial-number 98 "A" 0) INFO:: Command: (insertion-code-from-serial-number 98 "A" 0) INFO:: Command: (seqnum-from-serial-number 98 "A" 1) INFO:: Command: (insertion-code-from-serial-number 98 "A" 1) INFO:: Command: (seqnum-from-serial-number 98 "A" 2) INFO:: Command: (insertion-code-from-serial-number 98 "A" 2) INFO:: Command: (seqnum-from-serial-number 98 "A" 3) INFO:: Command: (insertion-code-from-serial-number 98 "A" 3) INFO:: Command: (seqnum-from-serial-number 98 "A" 4) INFO:: Command: (insertion-code-from-serial-number 98 "A" 4) INFO:: Command: (seqnum-from-serial-number 98 "A" 5) INFO:: Command: (insertion-code-from-serial-number 98 "A" 5) INFO:: Command: (seqnum-from-serial-number 98 "A" 6) INFO:: Command: (insertion-code-from-serial-number 98 "A" 6) INFO:: Command: (seqnum-from-serial-number 98 "A" 7) INFO:: Command: (insertion-code-from-serial-number 98 "A" 7) INFO:: Command: (seqnum-from-serial-number 98 "A" 8) INFO:: Command: (insertion-code-from-serial-number 98 "A" 8) INFO:: Command: (seqnum-from-serial-number 98 "A" 9) INFO:: Command: (insertion-code-from-serial-number 98 "A" 9) INFO:: Command: (seqnum-from-serial-number 98 "A" 10) INFO:: Command: (insertion-code-from-serial-number 98 "A" 10) INFO:: Command: (seqnum-from-serial-number 98 "A" 11) INFO:: Command: (insertion-code-from-serial-number 98 "A" 11) INFO:: Command: (seqnum-from-serial-number 98 "A" 12) INFO:: Command: (insertion-code-from-serial-number 98 "A" 12) INFO:: Command: (seqnum-from-serial-number 98 "A" 13) INFO:: Command: (insertion-code-from-serial-number 98 "A" 13) INFO:: Command: (seqnum-from-serial-number 98 "A" 14) INFO:: Command: (insertion-code-from-serial-number 98 "A" 14) INFO:: Command: (seqnum-from-serial-number 98 "A" 15) INFO:: Command: (insertion-code-from-serial-number 98 "A" 15) INFO:: Command: (seqnum-from-serial-number 98 "A" 16) INFO:: Command: (insertion-code-from-serial-number 98 "A" 16) INFO:: Command: (seqnum-from-serial-number 98 "A" 17) INFO:: Command: (insertion-code-from-serial-number 98 "A" 17) INFO:: Command: (seqnum-from-serial-number 98 "A" 18) INFO:: Command: (insertion-code-from-serial-number 98 "A" 18) INFO:: Command: (seqnum-from-serial-number 98 "A" 19) INFO:: Command: (insertion-code-from-serial-number 98 "A" 19) INFO:: Command: (seqnum-from-serial-number 98 "A" 20) INFO:: Command: (insertion-code-from-serial-number 98 "A" 20) INFO:: Command: (seqnum-from-serial-number 98 "A" 21) INFO:: Command: (insertion-code-from-serial-number 98 "A" 21) INFO:: Command: (seqnum-from-serial-number 98 "A" 22) INFO:: Command: (insertion-code-from-serial-number 98 "A" 22) INFO:: Command: (seqnum-from-serial-number 98 "A" 23) INFO:: Command: (insertion-code-from-serial-number 98 "A" 23) INFO:: Command: (seqnum-from-serial-number 98 "A" 24) INFO:: Command: (insertion-code-from-serial-number 98 "A" 24) INFO:: Command: (seqnum-from-serial-number 98 "A" 25) INFO:: Command: (insertion-code-from-serial-number 98 "A" 25) INFO:: Command: (seqnum-from-serial-number 98 "A" 26) INFO:: Command: (insertion-code-from-serial-number 98 "A" 26) INFO:: Command: (seqnum-from-serial-number 98 "A" 27) INFO:: Command: (insertion-code-from-serial-number 98 "A" 27) INFO:: Command: (seqnum-from-serial-number 98 "A" 28) INFO:: Command: (insertion-code-from-serial-number 98 "A" 28) INFO:: Command: (seqnum-from-serial-number 98 "A" 29) INFO:: Command: (insertion-code-from-serial-number 98 "A" 29) INFO:: Command: (seqnum-from-serial-number 98 "A" 30) INFO:: Command: (insertion-code-from-serial-number 98 "A" 30) INFO:: Command: (seqnum-from-serial-number 98 "A" 31) INFO:: Command: (insertion-code-from-serial-number 98 "A" 31) INFO:: Command: (seqnum-from-serial-number 98 "A" 32) INFO:: Command: (insertion-code-from-serial-number 98 "A" 32) INFO:: Command: (seqnum-from-serial-number 98 "A" 33) INFO:: Command: (insertion-code-from-serial-number 98 "A" 33) INFO:: Command: (seqnum-from-serial-number 98 "A" 34) INFO:: Command: (insertion-code-from-serial-number 98 "A" 34) INFO:: Command: (seqnum-from-serial-number 98 "A" 35) INFO:: Command: (insertion-code-from-serial-number 98 "A" 35) INFO:: Command: (seqnum-from-serial-number 98 "A" 36) INFO:: Command: (insertion-code-from-serial-number 98 "A" 36) INFO:: Command: (seqnum-from-serial-number 98 "A" 37) INFO:: Command: (insertion-code-from-serial-number 98 "A" 37) INFO:: Command: (seqnum-from-serial-number 98 "A" 38) INFO:: Command: (insertion-code-from-serial-number 98 "A" 38) INFO:: Command: (seqnum-from-serial-number 98 "A" 39) INFO:: Command: (insertion-code-from-serial-number 98 "A" 39) INFO:: Command: (seqnum-from-serial-number 98 "A" 40) INFO:: Command: (insertion-code-from-serial-number 98 "A" 40) INFO:: Command: (seqnum-from-serial-number 98 "A" 41) INFO:: Command: (insertion-code-from-serial-number 98 "A" 41) INFO:: Command: (seqnum-from-serial-number 98 "A" 42) INFO:: Command: (insertion-code-from-serial-number 98 "A" 42) INFO:: Command: (seqnum-from-serial-number 98 "A" 43) INFO:: Command: (insertion-code-from-serial-number 98 "A" 43) INFO:: Command: (seqnum-from-serial-number 98 "A" 44) INFO:: Command: (insertion-code-from-serial-number 98 "A" 44) INFO:: Command: (seqnum-from-serial-number 98 "A" 45) INFO:: Command: (insertion-code-from-serial-number 98 "A" 45) INFO:: Command: (seqnum-from-serial-number 98 "A" 46) INFO:: Command: (insertion-code-from-serial-number 98 "A" 46) INFO:: Command: (seqnum-from-serial-number 98 "A" 47) INFO:: Command: (insertion-code-from-serial-number 98 "A" 47) INFO:: Command: (seqnum-from-serial-number 98 "A" 48) INFO:: Command: (insertion-code-from-serial-number 98 "A" 48) INFO:: Command: (seqnum-from-serial-number 98 "A" 49) INFO:: Command: (insertion-code-from-serial-number 98 "A" 49) INFO:: Command: (seqnum-from-serial-number 98 "A" 50) INFO:: Command: (insertion-code-from-serial-number 98 "A" 50) INFO:: Command: (seqnum-from-serial-number 98 "A" 51) INFO:: Command: (insertion-code-from-serial-number 98 "A" 51) INFO:: Command: (seqnum-from-serial-number 98 "A" 52) INFO:: Command: (insertion-code-from-serial-number 98 "A" 52) INFO:: Command: (seqnum-from-serial-number 98 "A" 53) INFO:: Command: (insertion-code-from-serial-number 98 "A" 53) INFO:: Command: (seqnum-from-serial-number 98 "A" 54) INFO:: Command: (insertion-code-from-serial-number 98 "A" 54) INFO:: Command: (seqnum-from-serial-number 98 "A" 55) INFO:: Command: (insertion-code-from-serial-number 98 "A" 55) INFO:: Command: (seqnum-from-serial-number 98 "A" 56) INFO:: Command: (insertion-code-from-serial-number 98 "A" 56) INFO:: Command: (seqnum-from-serial-number 98 "A" 57) INFO:: Command: (insertion-code-from-serial-number 98 "A" 57) INFO:: Command: (seqnum-from-serial-number 98 "A" 58) INFO:: Command: (insertion-code-from-serial-number 98 "A" 58) INFO:: Command: (seqnum-from-serial-number 98 "A" 59) INFO:: Command: (insertion-code-from-serial-number 98 "A" 59) INFO:: Command: (seqnum-from-serial-number 98 "A" 60) INFO:: Command: (insertion-code-from-serial-number 98 "A" 60) INFO:: Command: (seqnum-from-serial-number 98 "A" 61) INFO:: Command: (insertion-code-from-serial-number 98 "A" 61) INFO:: Command: (seqnum-from-serial-number 98 "A" 62) INFO:: Command: (insertion-code-from-serial-number 98 "A" 62) INFO:: Command: (seqnum-from-serial-number 98 "A" 63) INFO:: Command: (insertion-code-from-serial-number 98 "A" 63) INFO:: Command: (seqnum-from-serial-number 98 "A" 64) INFO:: Command: (insertion-code-from-serial-number 98 "A" 64) INFO:: Command: (seqnum-from-serial-number 98 "A" 65) INFO:: Command: (insertion-code-from-serial-number 98 "A" 65) INFO:: Command: (seqnum-from-serial-number 98 "A" 66) INFO:: Command: (insertion-code-from-serial-number 98 "A" 66) INFO:: Command: (seqnum-from-serial-number 98 "A" 67) INFO:: Command: (insertion-code-from-serial-number 98 "A" 67) INFO:: Command: (seqnum-from-serial-number 98 "A" 68) INFO:: Command: (insertion-code-from-serial-number 98 "A" 68) INFO:: Command: (seqnum-from-serial-number 98 "A" 69) INFO:: Command: (insertion-code-from-serial-number 98 "A" 69) INFO:: Command: (seqnum-from-serial-number 98 "A" 70) INFO:: Command: (insertion-code-from-serial-number 98 "A" 70) INFO:: Command: (seqnum-from-serial-number 98 "A" 71) INFO:: Command: (insertion-code-from-serial-number 98 "A" 71) INFO:: Command: (seqnum-from-serial-number 98 "A" 72) INFO:: Command: (insertion-code-from-serial-number 98 "A" 72) INFO:: Command: (seqnum-from-serial-number 98 "A" 73) INFO:: Command: (insertion-code-from-serial-number 98 "A" 73) INFO:: Command: (seqnum-from-serial-number 98 "A" 74) INFO:: Command: (insertion-code-from-serial-number 98 "A" 74) INFO:: Command: (seqnum-from-serial-number 98 "A" 75) INFO:: Command: (insertion-code-from-serial-number 98 "A" 75) INFO:: Command: (seqnum-from-serial-number 98 "A" 76) INFO:: Command: (insertion-code-from-serial-number 98 "A" 76) INFO:: Command: (seqnum-from-serial-number 98 "A" 77) INFO:: Command: (insertion-code-from-serial-number 98 "A" 77) INFO:: Command: (seqnum-from-serial-number 98 "A" 78) INFO:: Command: (insertion-code-from-serial-number 98 "A" 78) INFO:: Command: (seqnum-from-serial-number 98 "A" 79) INFO:: Command: (insertion-code-from-serial-number 98 "A" 79) INFO:: Command: (seqnum-from-serial-number 98 "A" 80) INFO:: Command: (insertion-code-from-serial-number 98 "A" 80) INFO:: Command: (seqnum-from-serial-number 98 "A" 81) INFO:: Command: (insertion-code-from-serial-number 98 "A" 81) INFO:: Command: (seqnum-from-serial-number 98 "A" 82) INFO:: Command: (insertion-code-from-serial-number 98 "A" 82) INFO:: Command: (seqnum-from-serial-number 98 "A" 83) INFO:: Command: (insertion-code-from-serial-number 98 "A" 83) INFO:: Command: (seqnum-from-serial-number 98 "A" 84) INFO:: Command: (insertion-code-from-serial-number 98 "A" 84) INFO:: Command: (seqnum-from-serial-number 98 "A" 85) INFO:: Command: (insertion-code-from-serial-number 98 "A" 85) INFO:: Command: (seqnum-from-serial-number 98 "A" 86) INFO:: Command: (insertion-code-from-serial-number 98 "A" 86) INFO:: Command: (seqnum-from-serial-number 98 "A" 87) INFO:: Command: (insertion-code-from-serial-number 98 "A" 87) INFO:: Command: (seqnum-from-serial-number 98 "A" 88) INFO:: Command: (insertion-code-from-serial-number 98 "A" 88) INFO:: Command: (seqnum-from-serial-number 98 "A" 89) INFO:: Command: (insertion-code-from-serial-number 98 "A" 89) INFO:: Command: (seqnum-from-serial-number 98 "A" 90) INFO:: Command: (insertion-code-from-serial-number 98 "A" 90) INFO:: Command: (seqnum-from-serial-number 98 "A" 91) INFO:: Command: (insertion-code-from-serial-number 98 "A" 91) INFO:: Command: (seqnum-from-serial-number 98 "A" 92) INFO:: Command: (insertion-code-from-serial-number 98 "A" 92) INFO:: Command: (seqnum-from-serial-number 98 "B" 0) INFO:: Command: (insertion-code-from-serial-number 98 "B" 0) INFO:: Command: (seqnum-from-serial-number 98 "B" 1) INFO:: Command: (insertion-code-from-serial-number 98 "B" 1) INFO:: Command: (seqnum-from-serial-number 98 "B" 2) INFO:: Command: (insertion-code-from-serial-number 98 "B" 2) INFO:: Command: (seqnum-from-serial-number 98 "B" 3) INFO:: Command: (insertion-code-from-serial-number 98 "B" 3) INFO:: Command: (seqnum-from-serial-number 98 "B" 4) INFO:: Command: (insertion-code-from-serial-number 98 "B" 4) INFO:: Command: (seqnum-from-serial-number 98 "B" 5) INFO:: Command: 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(insertion-code-from-serial-number 98 "B" 90) INFO:: Command: (seqnum-from-serial-number 98 "B" 91) INFO:: Command: (insertion-code-from-serial-number 98 "B" 91) INFO:: Command: (seqnum-from-serial-number 98 "B" 92) INFO:: Command: (insertion-code-from-serial-number 98 "B" 92) INFO:: Command: (seqnum-from-serial-number 98 "B" 93) INFO:: Command: (insertion-code-from-serial-number 98 "B" 93) INFO:: Command: (seqnum-from-serial-number 98 "B" 94) INFO:: Command: (insertion-code-from-serial-number 98 "B" 94) INFO:: Command: (seqnum-from-serial-number 98 "B" 95) INFO:: Command: (insertion-code-from-serial-number 98 "B" 95) specs: 189 [[98, 'A', 1, ''], [98, 'A', 2, ''], [98, 'A', 3, ''], [98, 'A', 4, ''], [98, 'A', 5, ''], [98, 'A', 6, ''], [98, 'A', 7, ''], [98, 'A', 8, ''], [98, 'A', 9, ''], [98, 'A', 10, ''], [98, 'A', 11, ''], [98, 'A', 12, ''], [98, 'A', 13, ''], [98, 'A', 14, ''], [98, 'A', 15, ''], [98, 'A', 16, ''], [98, 'A', 17, ''], [98, 'A', 18, ''], [98, 'A', 19, ''], [98, 'A', 20, ''], [98, 'A', 21, ''], [98, 'A', 22, ''], [98, 'A', 23, ''], [98, 'A', 24, ''], [98, 'A', 25, ''], [98, 'A', 26, ''], [98, 'A', 27, ''], [98, 'A', 28, ''], [98, 'A', 29, ''], [98, 'A', 30, ''], [98, 'A', 31, ''], [98, 'A', 32, ''], [98, 'A', 33, ''], [98, 'A', 34, ''], [98, 'A', 35, ''], [98, 'A', 36, ''], [98, 'A', 37, ''], [98, 'A', 38, ''], [98, 'A', 39, ''], [98, 'A', 40, ''], [98, 'A', 41, ''], [98, 'A', 42, ''], [98, 'A', 43, ''], [98, 'A', 44, ''], [98, 'A', 45, ''], [98, 'A', 46, ''], [98, 'A', 47, ''], [98, 'A', 48, ''], [98, 'A', 49, ''], [98, 'A', 50, ''], [98, 'A', 51, ''], [98, 'A', 52, ''], [98, 'A', 53, ''], [98, 'A', 54, ''], [98, 'A', 55, ''], [98, 'A', 56, ''], [98, 'A', 57, ''], [98, 'A', 58, ''], [98, 'A', 59, ''], [98, 'A', 60, ''], [98, 'A', 61, ''], [98, 'A', 62, ''], [98, 'A', 63, ''], [98, 'A', 64, ''], [98, 'A', 65, ''], [98, 'A', 66, ''], [98, 'A', 67, ''], [98, 'A', 68, ''], [98, 'A', 69, ''], [98, 'A', 70, ''], [98, 'A', 71, ''], [98, 'A', 72, ''], [98, 'A', 73, ''], [98, 'A', 74, ''], [98, 'A', 75, ''], [98, 'A', 76, ''], [98, 'A', 77, ''], [98, 'A', 78, ''], [98, 'A', 79, ''], [98, 'A', 80, ''], [98, 'A', 81, ''], [98, 'A', 82, ''], [98, 'A', 83, ''], [98, 'A', 84, ''], [98, 'A', 85, ''], [98, 'A', 86, ''], [98, 'A', 87, ''], [98, 'A', 88, ''], [98, 'A', 89, ''], [98, 'A', 90, ''], [98, 'A', 91, ''], [98, 'A', 92, ''], [98, 'A', 93, ''], [98, 'B', 1, ''], [98, 'B', 2, ''], [98, 'B', 3, ''], [98, 'B', 4, ''], [98, 'B', 5, ''], [98, 'B', 6, ''], [98, 'B', 7, ''], [98, 'B', 8, ''], [98, 'B', 9, ''], [98, 'B', 10, ''], [98, 'B', 11, ''], [98, 'B', 12, ''], [98, 'B', 13, ''], [98, 'B', 14, ''], [98, 'B', 15, ''], [98, 'B', 16, ''], [98, 'B', 17, ''], [98, 'B', 18, ''], [98, 'B', 19, ''], [98, 'B', 20, ''], [98, 'B', 21, ''], [98, 'B', 22, ''], [98, 'B', 23, ''], [98, 'B', 24, ''], [98, 'B', 25, ''], [98, 'B', 26, ''], [98, 'B', 27, ''], [98, 'B', 28, ''], [98, 'B', 29, ''], [98, 'B', 30, ''], [98, 'B', 31, ''], [98, 'B', 32, ''], [98, 'B', 33, ''], [98, 'B', 34, ''], [98, 'B', 35, ''], [98, 'B', 36, ''], [98, 'B', 37, ''], [98, 'B', 38, ''], [98, 'B', 39, ''], [98, 'B', 40, ''], [98, 'B', 41, ''], [98, 'B', 42, ''], [98, 'B', 43, ''], [98, 'B', 44, ''], [98, 'B', 45, ''], [98, 'B', 46, ''], [98, 'B', 47, ''], [98, 'B', 48, ''], [98, 'B', 49, ''], [98, 'B', 50, ''], [98, 'B', 51, ''], [98, 'B', 52, ''], [98, 'B', 53, ''], [98, 'B', 54, ''], [98, 'B', 55, ''], [98, 'B', 56, ''], [98, 'B', 57, ''], [98, 'B', 58, ''], [98, 'B', 59, ''], [98, 'B', 60, ''], [98, 'B', 61, ''], [98, 'B', 62, ''], [98, 'B', 63, ''], [98, 'B', 64, ''], [98, 'B', 65, ''], [98, 'B', 66, ''], [98, 'B', 67, ''], [98, 'B', 68, ''], [98, 'B', 69, ''], [98, 'B', 70, ''], [98, 'B', 71, ''], [98, 'B', 72, ''], [98, 'B', 73, ''], [98, 'B', 74, ''], [98, 'B', 75, ''], [98, 'B', 76, ''], [98, 'B', 77, ''], [98, 'B', 78, ''], [98, 'B', 79, ''], [98, 'B', 80, ''], [98, 'B', 81, ''], [98, 'B', 82, ''], [98, 'B', 83, ''], [98, 'B', 84, ''], [98, 'B', 85, ''], [98, 'B', 86, ''], [98, 'B', 87, ''], [98, 'B', 88, ''], [98, 'B', 89, ''], [98, 'B', 90, ''], [98, 'B', 91, ''], [98, 'B', 92, ''], [98, 'B', 93, ''], [98, 'B', 94, ''], [98, 'B', 95, ''], [98, 'B', 96, '']] ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2goz-manip.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2goz-manip.pdb PDB file /home/paule/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 10/85 Molecule 99 read successfully DEBUG:: there were 7 types with no dictionary ok test60_0 (__main__.PdbMtzTestFunctions) post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok test61_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... INFO:: Command: (write-pdb-file 0 "rnase_zip_test.pdb.gz") INFO:: Command: (handle-read-draw-molecule-with-recentre "rnase_zip_test.pdb.gz" 1) gzip: stdout: Broken pipe gzip: stdout: Broken pipe INFO:: Reading coordinate file: rnase_zip_test.pdb.gz PDB file rnase_zip_test.pdb.gz has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 100 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 2 CB ok test62_0 (__main__.PdbMtzTestFunctions) Fix for Oliver Clarke fit by atom selection bug ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 101 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.50 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.02 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 2.98 Map minimum: ..... -0.88 INFO:: 0.00 seconds for contour map INFO:: 0.05 seconds in total masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_0.pdb.gz INFO:: replace_coords: 745 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it bl: 0.0363730669589 ok test999_0 (__main__.PdbMtzTestFunctions) Renumber residue range without overwriting coordinates. ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 103 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 103 "A" 10 20 -55) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_1.pdb.gz INFO:: Command: (renumber-residue-range 103 "A" 90 93 10) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_2.pdb.gz INFO:: Command: (renumber-residue-range 103 "A" 89 91 1) WARNING:: the new residue range overlaps with original one. Please change the range. Nothing has been done. INFO:: Command: (renumber-residue-range 103 "A" 80 91 12) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:23_2018_modification_3.pdb.gz INFO:: Command: (renumber-residue-range 103 "A" -100 200 9) ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/HOF.RES" 1) SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.90 13.70 9.24 90.00 98.21 90.00 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 104 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/HOF.RES") ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/hollander.ins" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.32 34.32 11.09 90.00 90.00 90.00 READ-INS:: Spacegroup: "I 41 2 2" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 105 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/hollander.ins") INFO:: spacegroup: I 41 2 2 ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.73 77.73 77.73 90.00 90.00 90.00 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 106 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/insulin.res") Map statistics: mean: -0.00 st.d: 0.31 Map statistics: min: -0.78, max: 6.08 -0.70 231 -0.52 4724 -0.35 24910 -0.18 55291 -0.01 95241 0.16 40930 0.33 7480 0.51 3968 0.68 2790 0.85 2117 1.02 1738 1.19 1221 1.36 888 1.53 595 1.71 355 1.88 240 2.05 137 2.22 97 2.39 62 2.56 46 2.73 17 2.91 17 3.08 13 3.25 10 3.42 7 3.59 1 3.76 3 3.94 7 4.11 2 4.28 5 4.45 1 4.62 2 4.79 2 4.96 0 5.14 1 5.31 0 5.48 0 5.65 0 5.82 0 5.99 1 6.16 0 Map statistics: mean: -0.00 st.d: 0.05 Map statistics: min: -0.21, max: 0.65 -0.20 7 -0.18 48 -0.16 209 -0.14 787 -0.11 2257 -0.09 5676 -0.07 12730 -0.05 24380 -0.03 38190 -0.01 46230 0.01 43880 0.04 32484 0.06 19420 0.08 9718 0.10 4120 0.12 1677 0.14 718 0.16 329 0.19 133 0.21 77 0.23 29 0.25 11 0.27 13 0.29 8 0.32 2 0.34 2 0.36 2 0.38 1 0.40 1 0.42 2 0.44 2 0.47 1 0.49 1 0.51 1 0.53 1 0.55 1 0.57 0 0.59 0 0.62 0 0.64 2 0.66 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... WARNING:: invalid molecule (204050) for write_shelx_ins_file WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... INFO:: Command: (update-go-to-atom-window-on-new-mol) ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... INFO:: Command: (update-go-to-atom-window-on-new-mol) fitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 2020 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Wed_Sep_19_11:45:25_2018_modification_0.res WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CD2" INFO:: backup file coot-backup/atom_selection_from_insulin.res_Wed_Sep_19_11:45:25_2018_modification_1.res WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CD2" INFO:: Command: (add-terminal-residue 110 "B" 2020 1) ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... INFO:: Command: (set-rotation-centre 3.00 -1.00 60.00) INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Wed_Sep_19_11:45:25_2018_modification_0.res WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3.00,-1.00,60.00) B-factor: 45.00 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (resname-from-serial-number 106 "D" 68) INFO:: Command: (seqnum-from-serial-number 106 "D" 68) INFO:: Command: (insertion-code-from-serial-number 106 "D" 68) ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... INFO:: Command: (n-chains 106) INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.60 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.31 INFO:: Using density cut-off: 0.18 (0.60 sigma) (mean -0.02 stdev: 0.11) INFO:: Blobs with volume larger than 11.00 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.40 3.20 INFO:: 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 28 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Wed_Sep_19_11:45:25_2018_modification_1.res WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" INFO:: Adding to solvent chain: D INFO:: Command: (n-chains 106) INFO:: Command: (resname-from-serial-number 106 "D" 96) INFO:: Command: (seqnum-from-serial-number 106 "D" 96) INFO:: Command: (insertion-code-from-serial-number 106 "D" 96) ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/miller/shelx-test4-NPD-mini.res" 1) 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 90.00 90.00 90.00 READ-INS:: Spacegroup: "P 21 21 21" INFO:: read_file() chain with chain id has 5 residues Symmetry available for this molecule Molecule 111 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/miller/shelx-test4-NPD-mini.res") INFO:: Command: (close-molecule 111) ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... INFO:: Command: (close-molecule 107) INFO:: Command: (close-molecule 106) ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/horma-p21.res" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90.00 101.73 90.00 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id has 23 residues Symmetry available for this molecule Molecule 112 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/horma-p21.res") WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " O1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C2 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C5 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" "CL1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " N1 " INFO:: SHELXL file new-horma.ins written. INFO:: Command: (handle-read-draw-molecule-with-recentre "new-horma.ins" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL debug:: ## new chain wiith chain-id A INFO:: CELL set to 14.08 32.76 18.66 90.00 101.73 90.00 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id A has 23 residues Symmetry available for this molecule Molecule 113 read successfully INFO:: Command: (read-shelx-ins-file "new-horma.ins") b_1: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] b_2: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/crash.hat" 0) LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 109.00 109.00 107.56 90.00 90.00 90.00 READ-INS:: Spacegroup: "I 4 2 2" INFO:: read_file() chain with chain id has 4 residues Symmetry available for this molecule Molecule 114 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/crash.hat") INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/crash.hat" 1) LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 109.00 109.00 107.56 90.00 90.00 90.00 READ-INS:: Spacegroup: "I 4 2 2" INFO:: read_file() chain with chain id has 4 residues Symmetry available for this molecule Molecule 115 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/crash.hat") ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... INFO:: Creating directory coot-ccp4 BL INFO:: run_command_in_dir dir:coot-ccp4 exe: /home/paule/ccp4/ccp4-6.3.0/bin/libcheck cl_args: [] data_lines: ['N', 'MON 3GP', ''] log_file: coot-libcheck-3GP.log # # --- 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 BL INFO:: libcheck status: 0 INFO:: libcheck-minimal? is False INFO:: Command: (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 0) INFO:: 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 in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 116 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Wed_Sep_19_11:45:31_2018_modification_0.pdb.gz Welcome to Coot INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Wed_Sep_19_11:45:31_2018_modification_1.pdb.gz INFO:: Command: (delete-residue-hydrogens 116 "A" 1 "" "") ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-3GP.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 117 read successfully DEBUG:: there were 0 types with no dictionary here 1 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Wed_Sep_19_11:45:32_2018_modification_0.pdb.gz ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/test-LIG.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb PDB file /home/paule/data/greg-data/test-LIG.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 118 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/test-LIG.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb PDB file /home/paule/data/greg-data/test-LIG.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 119 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-NPO.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 120 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (copy-molecule 120) INFO:: Command: (copy-molecule 120) INFO:: Command: (copy-molecule 120) INFO:: Command: (copy-molecule 120) INFO:: Command: (copy-molecule 120) INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /home/paule/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 in add_molecular_symmetry_matrices() made 0 biomt matrices 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 126 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making conventional map from MTZ filename /home/paule/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 1.50 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.14 seconds to read MTZ file INFO:: 0.09 seconds to initialize map INFO:: 0.08 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ -0.00 Map sigma: ....... 0.17 Map maximum: ..... 1.34 Map minimum: ..... -0.70 INFO:: 0.00 seconds for contour map INFO:: 0.34 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: making difference map from MTZ filename /home/paule/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 1.50 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.09 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.08 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.03 Map maximum: ..... 0.37 Map minimum: ..... -0.19 INFO:: 0.00 seconds for contour map INFO:: 0.18 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "DELFWT" "PHDELWT" "" 0 1 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: ligand number 0 is molecule number 120 with wiggly flag: 0 in execute_ligand_search_internal() import maps from mol 127 INFO:: Protein centre at: xyz = ( 58.29, 34.65, 30.63) Map statistics: mean: -0.02 st.d: 0.09 Map statistics: min: -0.70, max: 0.75 -0.68 6 -0.64 8 -0.60 27 -0.57 116 -0.53 354 -0.50 977 -0.46 1943 -0.42 3356 -0.39 5156 -0.35 6576 -0.31 7850 -0.28 8875 -0.24 9742 -0.21 11742 -0.17 16950 -0.13 29805 -0.10 58214 -0.06 102889 -0.02 142998 0.01 471776 0.05 106846 0.08 56087 0.12 21597 0.16 6911 0.19 2135 0.23 920 0.26 467 0.30 346 0.34 216 0.37 118 0.41 117 0.45 80 0.48 50 0.52 28 0.55 33 0.59 15 0.63 14 0.66 11 0.70 2 0.74 7 0.77 0 INFO:: find_clusters map_rms is 0.17 INFO:: Using density cut-off: 0.17 (1.00 sigma) (mean -0.02 stdev: 0.09) INFO:: Blobs with volume larger than 11.00 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.40 3.20 INFO:: Finding clusters...done debug:: n_ligands_for_cluster() top_score 4.04 and 4 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -51.61 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 93) at -137.41 Final Estimated RMS Z Scores: bonds: 0.11 angles: 0.04 torsions: N/A planes: 0.06 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 24.47 Refinement elapsed time: 0.02 INFO:: backup file coot-backup/Fitted_ligand_#0-0_Wed_Sep_19_11:45:35_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.02 and 8 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 16.73 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 28) at -74.11 Final Estimated RMS Z Scores: bonds: 0.05 angles: 0.05 torsions: N/A planes: 0.04 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 25.41 Refinement elapsed time: 0.07 INFO:: backup file coot-backup/Fitted_ligand_#1-0_Wed_Sep_19_11:45:36_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.09 and 4 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 12.49 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 79) at -66.82 Final Estimated RMS Z Scores: bonds: 0.06 angles: 0.03 torsions: N/A planes: 0.02 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 25.86 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/Fitted_ligand_#2-0_Wed_Sep_19_11:45:36_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.86 and 6 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 34.20 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 23) at -50.93 Final Estimated RMS Z Scores: bonds: 0.06 angles: 0.03 torsions: N/A planes: 0.05 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 26.53 Refinement elapsed time: 0.02 INFO:: backup file coot-backup/Fitted_ligand_#3-0_Wed_Sep_19_11:45:37_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.39 and 10 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 51.68 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 17) at -59.94 Final Estimated RMS Z Scores: bonds: 0.08 angles: 0.03 torsions: N/A planes: 0.09 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 27.65 Refinement elapsed time: 0.05 INFO:: backup file coot-backup/Fitted_ligand_#4-0_Wed_Sep_19_11:45:38_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.68 and 8 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -0.94 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 92) at -118.22 Final Estimated RMS Z Scores: bonds: 0.09 angles: 0.09 torsions: N/A planes: 0.15 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 28.55 Refinement elapsed time: 0.03 INFO:: backup file coot-backup/Fitted_ligand_#5-0_Wed_Sep_19_11:45:39_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.10 and 8 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 10.37 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 34) at -74.97 Final Estimated RMS Z Scores: bonds: 0.05 angles: 0.04 torsions: N/A planes: 0.10 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 29.43 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/Fitted_ligand_#6-0_Wed_Sep_19_11:45:40_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.64 and 8 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 29.49 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 87) at -164.10 Final Estimated RMS Z Scores: bonds: 0.09 angles: 0.10 torsions: N/A planes: 0.08 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 30.38 Refinement elapsed time: 0.08 INFO:: backup file coot-backup/Fitted_ligand_#7-0_Wed_Sep_19_11:45:41_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.07 and 3 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 13.06 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 89) at -92.78 Final Estimated RMS Z Scores: bonds: 0.13 angles: 0.14 torsions: N/A planes: 0.06 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 30.78 Refinement elapsed time: 0.06 INFO:: backup file coot-backup/Fitted_ligand_#8-0_Wed_Sep_19_11:45:41_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.86 and 5 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 21.14 Initial RMS Z values bonds: 2.32 angles: 0.03 torsions: N/A planes: 0.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 129) at -65.83 Final Estimated RMS Z Scores: bonds: 0.03 angles: 0.01 torsions: N/A planes: 0.07 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 31.34 Refinement elapsed time: 0.02 INFO:: backup file coot-backup/Fitted_ligand_#9-0_Wed_Sep_19_11:45:42_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:969): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Fitting NPO gave these results: [130, 131, 132, 133, 134, 135, 136, 137, 138, 139] ok test08_0 (__main__.LigandTestFunctions) Test dipole ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/dipole-residues.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/dipole-residues.pdb PDB file /home/paule/data/greg-data/dipole-residues.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 140 read successfully DEBUG:: there were 0 types with no dictionary info:: dipole components [-2.219999939203263, 4.440892098500626e-16, 0.0] ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints ok test10_0 (__main__.LigandTestFunctions) Pyrogen Runs OK? ... ok test11_0 (__main__.LigandTestFunctions) pyrogen dictionary does not make double-quoted atom names ... ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 141 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 141 INFO:: Command: (assign-pir-sequence 141 "A" ">test ACDEFGHIKLMNPQ*") debug seq ACDEFGHIKLMNPQ storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 141 INFO:: Command: (assign-pir-sequence 141 "A" ">test ACDEFGHIKLMNPQRST*") ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb PDB file /home/paule/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 in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 142 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.50 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.02 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 2.98 Map minimum: ..... -0.88 INFO:: 0.00 seconds for contour map INFO:: 0.05 seconds in total storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 142 INFO:: Command: (assign-pir-sequence 142 "A" "> tutorial-modern chain A RNASE DVSGTVCLSA LPPEATDTLN LIASDGPFPY SQDGVVFQNR ESVLPTQSYG YYHEYTVITP GARTRGTRRI ICGEATQEDY YTGDHYATFS LID * ") INFO:: Command: (set-rotation-centre 64.27 7.04 14.42) Cootaneering: imol 142 chain-id B resno 60 inscode at-name CA alt-conf Sequence: ?EYTVITPGARTR Confidence: 1.00 From : HEYTVITPGARTR Chain id: 0 Offset: 53 INFO:: backup file coot-backup/_home_paule_data_greg-data_crashes_on_cootaneering-v2.pdb_Wed_Sep_19_11:45:43_2018_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:: thrown Null previous residue WARNING:: no rotamers probabilities for residue type GLY INFO:: replace_coords: 12 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: 15 atoms updated. INFO:: replace_coords: 10 atoms updated. INFO:: replace_coords: 10 atoms updated. INFO:: replace_coords: 11 atoms updated. INFO:: replace_coords: 10 atoms updated. INFO:: replace_coords: 10 atoms updated. WARNING:: thrown Failed to get a good fitting result WARNING:: no rotamers probabilities for residue type GLY WARNING:: thrown Failed to get a good fitting result WARNING:: no rotamers probabilities for residue type ALA INFO:: replace_coords: 14 atoms updated. INFO:: replace_coords: 10 atoms updated. WARNING:: thrown Null next residue INFO:: replace_coords: 11 atoms updated. ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.33 max devi: 0.54 min devi: 0.08 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.01 rms devi: 0.01 max devi: 0.02 min devi: 0.00 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.32 max devi: 0.50 min devi: 0.11 INFO:: 5 matched atoms had: mean devi: 0.27 rms devi: 0.34 max devi: 0.54 min devi: 0.08 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Sep_19_11:45:43_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: Command: (copy-molecule 144) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 76.27 10.04 14.42) INFO:: Command: (go-to-view-number 2 1) INFO:: Command: (n-chains 145) INFO:: Command: (chain_id 145 0) INFO:: Command: (chain_id 145 1) INFO:: Command: (is-solvent-chain-p 145 "A") There are 8 residues in chain A INFO:: Command: (resname-from-serial-number 145 "A" 0) INFO:: Command: (seqnum-from-serial-number 145 "A" 0) INFO:: Command: (insertion-code-from-serial-number 145 "A" 0) INFO:: Command: (resname-from-serial-number 145 "A" 1) INFO:: Command: (seqnum-from-serial-number 145 "A" 1) INFO:: Command: (insertion-code-from-serial-number 145 "A" 1) INFO:: Command: (resname-from-serial-number 145 "A" 2) INFO:: Command: (seqnum-from-serial-number 145 "A" 2) INFO:: Command: (insertion-code-from-serial-number 145 "A" 2) INFO:: Command: (resname-from-serial-number 145 "A" 3) INFO:: Command: (seqnum-from-serial-number 145 "A" 3) INFO:: Command: (insertion-code-from-serial-number 145 "A" 3) INFO:: Command: (resname-from-serial-number 145 "A" 4) INFO:: Command: (seqnum-from-serial-number 145 "A" 4) INFO:: Command: (insertion-code-from-serial-number 145 "A" 4) INFO:: Command: (resname-from-serial-number 145 "A" 5) INFO:: Command: (seqnum-from-serial-number 145 "A" 5) INFO:: Command: (insertion-code-from-serial-number 145 "A" 5) INFO:: Command: (resname-from-serial-number 145 "A" 6) INFO:: Command: (seqnum-from-serial-number 145 "A" 6) INFO:: Command: (insertion-code-from-serial-number 145 "A" 6) INFO:: Command: (resname-from-serial-number 145 "A" 7) INFO:: Command: (seqnum-from-serial-number 145 "A" 7) INFO:: Command: (insertion-code-from-serial-number 145 "A" 7) INFO:: Command: (is-solvent-chain-p 145 "B") There are 8 residues in chain B INFO:: Command: (resname-from-serial-number 145 "B" 0) INFO:: Command: (seqnum-from-serial-number 145 "B" 0) INFO:: Command: (insertion-code-from-serial-number 145 "B" 0) INFO:: Command: (resname-from-serial-number 145 "B" 1) INFO:: Command: (seqnum-from-serial-number 145 "B" 1) INFO:: Command: (insertion-code-from-serial-number 145 "B" 1) INFO:: Command: (resname-from-serial-number 145 "B" 2) INFO:: Command: (seqnum-from-serial-number 145 "B" 2) INFO:: Command: (insertion-code-from-serial-number 145 "B" 2) INFO:: Command: (resname-from-serial-number 145 "B" 3) INFO:: Command: (seqnum-from-serial-number 145 "B" 3) INFO:: Command: (insertion-code-from-serial-number 145 "B" 3) INFO:: Command: (resname-from-serial-number 145 "B" 4) INFO:: Command: (seqnum-from-serial-number 145 "B" 4) INFO:: Command: (insertion-code-from-serial-number 145 "B" 4) INFO:: Command: (resname-from-serial-number 145 "B" 5) INFO:: Command: (seqnum-from-serial-number 145 "B" 5) INFO:: Command: (insertion-code-from-serial-number 145 "B" 5) INFO:: Command: (resname-from-serial-number 145 "B" 6) INFO:: Command: (seqnum-from-serial-number 145 "B" 6) INFO:: Command: (insertion-code-from-serial-number 145 "B" 6) INFO:: Command: (resname-from-serial-number 145 "B" 7) INFO:: Command: (seqnum-from-serial-number 145 "B" 7) INFO:: Command: (insertion-code-from-serial-number 145 "B" 7) INFO:: Command: (copy-molecule 144) INFO:: Matching/moving molecule number 146 to 146 INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 0.00 rms devi: 0.00 max devi: 0.00 min devi: 0.00 INFO:: Axis orientation: ( 0.6857, -0.6005, -0.4114) INFO:: Rotation in CCP4 Polar Angles: Polar = ( 0, 0, 0) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Wed_Sep_19_11:45:43_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 1,-9.556e-09, 1.395e-08| | 9.556e-09, 1, 1.593e-08| |-1.395e-08,-1.593e-08, 1| ( -24.14, -24.14, -24.14) No unit cell for this molecule, hence no fractional matrix. INFO:: Command: (go-to-view-number 3 1) ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/1wly.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/1wly.pdb PDB file /home/paule/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 147 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/1yb5.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/1yb5.pdb PDB file /home/paule/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices 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 148 read successfully DEBUG:: there were 2 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: Command: (graphics-to-ca-plus-ligands-representation 147) INFO:: Command: (graphics-to-ca-plus-ligands-representation 148) INFO:: reference 147 has 750 atoms selected INFO:: moving 148 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance(/A) A 6 A 7 A 8 <---> A 2 : 0.7510 A 9 <---> A 3 : 0.9422 A 10 <---> A 4 : 0.6300 A 11 <---> A 5 : 0.7119 A 12 <---> A 6 : 0.6310 A 13 <---> A 7 : 0.4675 A 14 <---> A 8 : 0.4264 A 15 <---> A 9 : 0.9792 A 16 <---> A 10 : 0.7549 A 17 <---> A 11 : 0.4884 A 18 <---> A 12 : 0.7451 A 19 <---> A 13 : 0.4606 A 20 <---> A 14 : 1.2809 A 21 <---> A 15 : 1.2412 A 22 <---> A 16 : 1.0733 A 23 <---> A 17 : 0.9730 A 24 <---> A 18 : 0.4705 A 25 <---> A 19 : 0.3560 A 26 <---> A 20 : 3.1145 A 27 A 28 <---> A 21 : 1.5754 A 29 <---> A 22 : 1.6322 A 30 A 31 <---> A 23 : 1.9973 A 32 <---> A 25 : 1.8324 A 33 <---> A 26 : 0.9310 A 34 <---> A 27 : 0.6808 A 35 <---> A 28 : 0.2674 A 36 <---> A 29 : 0.5995 A 37 <---> A 30 : 0.6992 A 38 <---> A 31 : 0.8620 A 39 <---> A 32 : 0.8421 A 40 <---> A 33 : 0.7208 A 41 <---> A 34 : 0.8681 A 42 <---> A 35 : 0.7781 A 43 <---> A 36 : 0.6211 A 44 <---> A 37 : 0.4657 A 45 <---> A 38 : 0.7475 A 46 <---> A 39 : 0.5170 A 47 <---> A 40 : 0.5058 A 48 <---> A 41 : 0.8897 A 49 <---> A 42 : 0.5835 A 50 <---> A 43 : 0.4347 A 51 <---> A 44 : 0.6192 A 52 <---> A 45 : 0.2150 A 53 <---> A 46 : 0.7474 A 54 <---> A 47 : 1.0213 A 55 <---> A 48 : 0.9208 A 56 <---> A 49 : 0.9392 A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 0.4666 A 66 <---> A 61 : 0.0523 A 67 <---> A 62 : 1.0719 A 68 <---> A 63 : 0.7933 A 69 <---> A 64 : 0.8916 A 70 <---> A 65 : 1.2580 A 71 <---> A 66 : 0.6932 A 72 <---> A 67 : 1.0345 A 73 <---> A 68 : 1.4417 A 74 <---> A 69 : 0.9092 A 75 <---> A 70 : 1.6166 A 76 <---> A 71 : 0.8741 A 77 <---> A 72 : 0.2388 A 78 <---> A 73 : 0.3118 A 79 <---> A 74 : 0.3887 A 80 <---> A 75 : 0.7613 A 81 <---> A 76 : 0.9044 A 82 <---> A 77 : 0.6090 A 83 <---> A 78 : 1.7978 A 84 <---> A 79 : 1.9256 A 85 <---> A 80 : 1.3416 A 86 <---> A 81 : 0.5658 A 87 <---> A 82 : 0.4480 A 88 <---> A 83 : 0.9078 A 89 <---> A 84 : 0.3625 A 90 <---> A 85 : 0.4040 A 91 <---> A 86 : 0.4586 A 92 <---> A 87 : 0.4340 A 93 <---> A 88 : 0.3664 A 94 <---> A 89 : 0.4921 A 95 <---> A 90 : 0.6498 A 96 <---> A 91 : 1.5805 A 97 <---> A 92 : 2.8839 A 98 A 99 A 100 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI INFO:: backup file coot-backup/_home_paule_data_greg-data_1yb5.pdb_Wed_Sep_19_11:45:44_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal 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 101.0220 169.7385 Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277 Translation - Angstroms 70.6538 7.7930 21.2852 INFO: core rmsd achieved: 1.0199 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: 4.0000 sequence identity: 30.5263% INFO:: Command: (set-rotation-centre 65.65 -3.00 -4.00) INFO:: Command: (go-to-view-number 4 1) ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/1pyd.pdb" 0) WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb INFO:: Command: (graphics-to-ca-plus-ligands-representation -1) INFO:: Command: (set-graphics-window-size 678 452) INFO:: Command: (molecule-name 0) 0 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 1) 1 /home/paule/data/greg-data/ins-code-fragment-pre.pdb INFO:: Command: (molecule-name 2) 2 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 3) 3 PTR_from_dict 4 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 5 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 6) 6 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 7) 7 mainchain-forward INFO:: Command: (molecule-name 8) 8 /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: Command: (molecule-name 9) 9 regression-test-terminal-residue.pdb INFO:: Command: (molecule-name 10) 10 atom selection from regression-test-terminal-residue.pdb INFO:: Command: (molecule-name 11) 11 /home/paule/data/greg-data/frag-2wot.pdb INFO:: Command: (molecule-name 12) 12 /home/paule/data/greg-data/tutorial-modern.pdb 13 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 14) 14 sphere selection from tutorial-modern.pdb INFO:: Command: (molecule-name 15) 15 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 17) 17 /home/paule/data/greg-data/rotamer-test-fragment.pdb INFO:: Command: (molecule-name 18) 18 /home/paule/data/greg-data/res098.pdb INFO:: Command: (molecule-name 19) 19 /home/paule/data/greg-data/tutorial-modern.pdb 20 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 21) 21 /home/paule/data/greg-data/pdb3knw.ent INFO:: Command: (molecule-name 22) 22 /home/paule/data/greg-data/pdb1py3.ent INFO:: Command: (molecule-name 25) 25 /home/paule/data/greg-data/alt-conf-pepflip-test.pdb INFO:: Command: (molecule-name 26) 26 /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb INFO:: Command: (molecule-name 29) 29 /home/paule/data/greg-data/tutorial-modern.pdb 30 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 31) 31 /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: Command: (molecule-name 32) 32 /home/paule/data/greg-data/tutorial-modern.pdb 33 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 34) 34 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 35) 35 /home/paule/data/greg-data/alt-conf-waters.pdb INFO:: Command: (molecule-name 36) 36 /home/paule/data/greg-data/backrub-fragment.pdb INFO:: Command: (molecule-name 37) 37 Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb 38 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT INFO:: Command: (molecule-name 39) 39 /home/paule/data/greg-data/test-TER-OXT.pdb INFO:: Command: (molecule-name 40) 40 /home/paule/data/greg-data/val.pdb INFO:: Command: (molecule-name 41) 41 /home/paule/data/greg-data/2yie-frag.pdb INFO:: Command: (molecule-name 42) 42 /home/paule/data/greg-data/4f8g.pdb INFO:: Command: (molecule-name 43) 43 /home/paule/data/greg-data/4f8g.pdb 44 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 45 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 46) 46 /home/paule/data/greg-data/tutorial-modern.pdb 47 Generic Masked Map 48 difference-map 51 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 52 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 53 averaged-map 54 difference-map INFO:: Command: (molecule-name 55) 55 /home/paule/data/greg-data/multi-carbo-coot-3.pdb INFO:: Command: (molecule-name 56) 56 /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb 57 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 58) 58 /home/paule/data/greg-data/monomer-VAL.pdb INFO:: Command: (molecule-name 59) 59 /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb INFO:: Command: (molecule-name 60) 60 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 61) 61 /home/paule/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 62) 62 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 63) 63 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 64) 64 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 65) 65 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 66) 66 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 67) 67 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 68) 68 /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb INFO:: Command: (molecule-name 69) 69 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 70) 70 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 71) 71 /home/paule/data/greg-data/pdb3hfl.ent 72 /home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT INFO:: Command: (molecule-name 73) 73 Ideal-A-form-RNA INFO:: Command: (molecule-name 74) 74 Ideal-A-form-RNA INFO:: Command: (molecule-name 75) 75 Ideal-A-form-DNA INFO:: Command: (molecule-name 76) 76 Ideal-A-form-DNA INFO:: Command: (molecule-name 77) 77 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 78) 78 /home/paule/data/greg-data/some-waters-with-ter.pdb INFO:: Command: (molecule-name 79) 79 /home/paule/data/greg-data/tm+some-waters.pdb INFO:: Command: (molecule-name 80) 80 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 81) 81 /home/paule/data/greg-data/water-test-no-cell.pdb INFO:: Command: (molecule-name 82) 82 /home/paule/data/greg-data/pathological-water-test.pdb INFO:: Command: (molecule-name 83) 83 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb 84 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 85) 85 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 86) 86 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 87) 87 /home/paule/data/greg-data/pdb1hvv.ent INFO:: Command: (molecule-name 88) 88 /home/paule/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 89) 89 /home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 90) 90 SymOp_-X,-X+Y,-Z+1/3_Copy_of_87 INFO:: Command: (molecule-name 91) 91 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 92) 92 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 93) 93 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 94) 94 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 95) 95 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 96) 96 /home/paule/data/greg-data/pdb1py3.ent INFO:: Command: (molecule-name 97) 97 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 98) 98 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 99) 99 /home/paule/data/greg-data/2goz-manip.pdb INFO:: Command: (molecule-name 100) 100 rnase_zip_test.pdb.gz INFO:: Command: (molecule-name 101) 101 /home/paule/data/greg-data/tutorial-modern.pdb 102 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 103) 103 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 104) 104 /home/paule/data/greg-data/HOF.RES INFO:: Command: (molecule-name 105) 105 /home/paule/data/greg-data/hollander.ins 108 /home/paule/data/greg-data/insulin.fcf Diff-SigmaA INFO:: Command: (molecule-name 109) 109 atom selection from insulin.res INFO:: Command: (molecule-name 110) 110 atom selection from insulin.res INFO:: Command: (molecule-name 112) 112 /home/paule/data/greg-data/horma-p21.res INFO:: Command: (molecule-name 113) 113 new-horma.ins INFO:: Command: (molecule-name 114) 114 /home/paule/data/greg-data/crash.hat INFO:: Command: (molecule-name 115) 115 /home/paule/data/greg-data/crash.hat INFO:: Command: (molecule-name 116) 116 coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 117) 117 /home/paule/data/greg-data/monomer-3GP.pdb INFO:: Command: (molecule-name 118) 118 /home/paule/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 119) 119 /home/paule/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 120) 120 /home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 121) 121 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 122) 122 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 123) 123 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 124) 124 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 125) 125 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 126) 126 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb 127 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT 128 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT 129 Masked (by protein) INFO:: Command: (molecule-name 130) 130 Fitted ligand #0-0 INFO:: Command: (molecule-name 131) 131 Fitted ligand #1-0 INFO:: Command: (molecule-name 132) 132 Fitted ligand #2-0 INFO:: Command: (molecule-name 133) 133 Fitted ligand #3-0 INFO:: Command: (molecule-name 134) 134 Fitted ligand #4-0 INFO:: Command: (molecule-name 135) 135 Fitted ligand #5-0 INFO:: Command: (molecule-name 136) 136 Fitted ligand #6-0 INFO:: Command: (molecule-name 137) 137 Fitted ligand #7-0 INFO:: Command: (molecule-name 138) 138 Fitted ligand #8-0 INFO:: Command: (molecule-name 139) 139 Fitted ligand #9-0 INFO:: Command: (molecule-name 140) 140 /home/paule/data/greg-data/dipole-residues.pdb INFO:: Command: (molecule-name 141) 141 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 142) 142 /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb 143 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 144) 144 Ideal-A-form-RNA INFO:: Command: (molecule-name 145) 145 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 146) 146 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 147) 147 /home/paule/data/greg-data/1wly.pdb INFO:: Command: (molecule-name 148) 148 /home/paule/data/greg-data/1yb5.pdb INFO:: Command: (graphics-to-ca-plus-ligands-representation 148) ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2qd9.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2qd9.pdb PDB file /home/paule/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 149 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2gtn.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2gtn.pdb PDB file /home/paule/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 0/337 Molecule 150 read successfully DEBUG:: there were 1 types with no dictionary INFO:: reference 149 has 169 atoms selected INFO:: moving 150 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_home_paule_data_greg-data_2gtn.pdb_Wed_Sep_19_11:45:44_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal 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) 116.8035 -94.6984 1.2491 Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832 Translation - Angstroms 0.3207 0.6598 0.8819 INFO: core rmsd achieved: 0.2210 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: 1.0000 sequence identity: 100.0000% ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0510 seconds in total INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.8760,16.1670,23.0330) B-factor: 20.0300 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.1788 rms devi: 4.8592 max devi: 46.2590 min devi: 0.1254 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 4 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 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 409600 out of 409600 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0006 st.d: 0.3256 Map statistics: min: -1.4696, max: 2.2923 -1.4225 2 -1.3285 5 -1.2344 5 -1.1404 10 -1.0463 9 -0.9523 37 -0.8583 141 -0.7642 493 -0.6702 1554 -0.5761 4667 -0.4821 12350 -0.3880 26465 -0.2940 43650 -0.1999 55555 -0.1059 57553 -0.0118 50690 0.0822 40145 0.1763 30074 0.2703 23268 0.3644 17859 0.4584 13062 0.5524 9524 0.6465 7028 0.7405 4917 0.8346 3611 0.9286 2439 1.0227 1610 1.1167 1087 1.2108 736 1.3048 442 1.3989 252 1.4929 160 1.5870 83 1.6810 49 1.7751 24 1.8691 17 1.9631 13 2.0572 4 2.1512 5 2.2453 5 2.3393 0 INFO:: installing ghost map with name :Map 151 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 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0004 st.d: 0.3236 Map statistics: min: -1.4496, max: 2.3411 -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 2 2.3885 0 ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... NCS info: [['A', 'B']] ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 156 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/insulin.res") no diffs NCS target chain has 93 peers. ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices 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 157 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:45_2018_modification_0.pdb.gz INFO:: Command: (delete-residue 157 "B" 1 "") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:45_2018_modification_1.pdb.gz INFO:: Command: (delete-residue 157 "B" 2 "") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:45_2018_modification_2.pdb.gz INFO:: Command: (delete-residue 157 "B" 3 "") INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 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" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 157 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 157 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 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) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:45_2018_modification_3.pdb.gz INFO:: Command: (seqnum-from-serial-number 157 "B" 0) INFO:: Command: (seqnum-from-serial-number 157 "B" 1) INFO:: Command: (seqnum-from-serial-number 157 "B" 2) INFO:: Command: (seqnum-from-serial-number 157 "B" 3) INFO:: Command: (seqnum-from-serial-number 157 "B" 4) INFO:: Command: (seqnum-from-serial-number 157 "B" 5) INFO:: Command: (seqnum-from-serial-number 157 "B" 6) INFO:: Command: (seqnum-from-serial-number 157 "B" 7) INFO:: Command: (seqnum-from-serial-number 157 "B" 8) INFO:: Command: (seqnum-from-serial-number 157 "B" 9) INFO:: Command: (seqnum-from-serial-number 157 "B" 10) INFO:: Command: (seqnum-from-serial-number 157 "B" 11) INFO:: Command: (seqnum-from-serial-number 157 "B" 12) INFO:: Command: (seqnum-from-serial-number 157 "B" 13) INFO:: Command: (seqnum-from-serial-number 157 "B" 14) INFO:: Command: (seqnum-from-serial-number 157 "B" 15) INFO:: Command: (seqnum-from-serial-number 157 "B" 16) INFO:: Command: (seqnum-from-serial-number 157 "B" 17) INFO:: Command: (seqnum-from-serial-number 157 "B" 18) INFO:: Command: (seqnum-from-serial-number 157 "B" 19) INFO:: Command: (seqnum-from-serial-number 157 "B" 20) INFO:: Command: (seqnum-from-serial-number 157 "B" 21) INFO:: Command: (seqnum-from-serial-number 157 "B" 22) INFO:: Command: (seqnum-from-serial-number 157 "B" 23) INFO:: Command: (seqnum-from-serial-number 157 "B" 24) INFO:: Command: (seqnum-from-serial-number 157 "B" 25) INFO:: Command: (seqnum-from-serial-number 157 "B" 26) INFO:: Command: (seqnum-from-serial-number 157 "B" 27) INFO:: Command: (seqnum-from-serial-number 157 "B" 28) INFO:: Command: (seqnum-from-serial-number 157 "B" 29) INFO:: Command: (seqnum-from-serial-number 157 "B" 30) INFO:: Command: (seqnum-from-serial-number 157 "B" 31) INFO:: Command: (seqnum-from-serial-number 157 "B" 32) INFO:: Command: (seqnum-from-serial-number 157 "B" 33) INFO:: Command: (seqnum-from-serial-number 157 "B" 34) INFO:: Command: (seqnum-from-serial-number 157 "B" 35) INFO:: Command: (seqnum-from-serial-number 157 "B" 36) INFO:: Command: (seqnum-from-serial-number 157 "B" 37) INFO:: Command: (seqnum-from-serial-number 157 "B" 38) INFO:: Command: (seqnum-from-serial-number 157 "B" 39) INFO:: Command: (seqnum-from-serial-number 157 "B" 40) INFO:: Command: (seqnum-from-serial-number 157 "B" 41) INFO:: Command: (seqnum-from-serial-number 157 "B" 42) INFO:: Command: (seqnum-from-serial-number 157 "B" 43) INFO:: Command: (seqnum-from-serial-number 157 "B" 44) INFO:: Command: (seqnum-from-serial-number 157 "B" 45) INFO:: Command: (seqnum-from-serial-number 157 "B" 46) INFO:: Command: (seqnum-from-serial-number 157 "B" 47) INFO:: Command: (seqnum-from-serial-number 157 "B" 48) INFO:: Command: (seqnum-from-serial-number 157 "B" 49) INFO:: Command: (seqnum-from-serial-number 157 "B" 50) INFO:: Command: (seqnum-from-serial-number 157 "B" 51) INFO:: Command: (seqnum-from-serial-number 157 "B" 52) INFO:: Command: (seqnum-from-serial-number 157 "B" 53) INFO:: Command: (seqnum-from-serial-number 157 "B" 54) INFO:: Command: (seqnum-from-serial-number 157 "B" 55) INFO:: Command: (seqnum-from-serial-number 157 "B" 56) INFO:: Command: (seqnum-from-serial-number 157 "B" 57) INFO:: Command: (seqnum-from-serial-number 157 "B" 58) INFO:: Command: (seqnum-from-serial-number 157 "B" 59) INFO:: Command: (seqnum-from-serial-number 157 "B" 60) INFO:: Command: (seqnum-from-serial-number 157 "B" 61) INFO:: Command: (seqnum-from-serial-number 157 "B" 62) INFO:: Command: (seqnum-from-serial-number 157 "B" 63) INFO:: Command: (seqnum-from-serial-number 157 "B" 64) INFO:: Command: (seqnum-from-serial-number 157 "B" 65) INFO:: Command: (seqnum-from-serial-number 157 "B" 66) INFO:: Command: (seqnum-from-serial-number 157 "B" 67) INFO:: Command: (seqnum-from-serial-number 157 "B" 68) INFO:: Command: (seqnum-from-serial-number 157 "B" 69) INFO:: Command: (seqnum-from-serial-number 157 "B" 70) INFO:: Command: (seqnum-from-serial-number 157 "B" 71) INFO:: Command: (seqnum-from-serial-number 157 "B" 72) INFO:: Command: (seqnum-from-serial-number 157 "B" 73) INFO:: Command: (seqnum-from-serial-number 157 "B" 74) INFO:: Command: (seqnum-from-serial-number 157 "B" 75) INFO:: Command: (seqnum-from-serial-number 157 "B" 76) INFO:: Command: (seqnum-from-serial-number 157 "B" 77) INFO:: Command: (seqnum-from-serial-number 157 "B" 78) INFO:: Command: (seqnum-from-serial-number 157 "B" 79) INFO:: Command: (seqnum-from-serial-number 157 "B" 80) INFO:: Command: (seqnum-from-serial-number 157 "B" 81) INFO:: Command: (seqnum-from-serial-number 157 "B" 82) INFO:: Command: (seqnum-from-serial-number 157 "B" 83) INFO:: Command: (seqnum-from-serial-number 157 "B" 84) INFO:: Command: (seqnum-from-serial-number 157 "B" 85) INFO:: Command: (seqnum-from-serial-number 157 "B" 86) INFO:: Command: (seqnum-from-serial-number 157 "B" 87) INFO:: Command: (seqnum-from-serial-number 157 "B" 88) INFO:: Command: (seqnum-from-serial-number 157 "B" 89) INFO:: Command: (seqnum-from-serial-number 157 "B" 90) INFO:: Command: (seqnum-from-serial-number 157 "B" 91) INFO:: Command: (seqnum-from-serial-number 157 "B" 92) INFO:: Command: (seqnum-from-serial-number 157 "B" 93) INFO:: Command: (seqnum-from-serial-number 157 "B" 94) INFO:: Command: (seqnum-from-serial-number 157 "B" 95) INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:45_2018_modification_4.pdb.gz INFO:: Command: (mutate 157 "A" 2 "" "TRP") DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 157 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 157 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:45_2018_modification_5.pdb.gz ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1t6q.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1t6q.ent PDB file /home/paule/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices 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 158 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Wed_Sep_19_11:45:45_2018_modification_0.pdb.gz INFO:: Command: (mutate 158 "A" 50 "" "ASP") INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 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: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 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:: Command: (is-solvent-chain-p 158 "C") DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 158 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 158 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 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) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 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) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Wed_Sep_19_11:45:45_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Wed_Sep_19_11:45:45_2018_modification_2.pdb.gz result: [True, True] ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices 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 159 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 159 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: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 540 in second selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.4989 rms devi: 2.7962 max devi: 6.6860 min devi: 0.4401 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: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.6728 rms devi: 2.9369 max devi: 6.1200 min devi: 0.2483 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: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 1.7317 rms devi: 1.9769 max devi: 7.9453 min devi: 0.5297 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 INFO:: Command: (copy-molecule 159) INFO:: Matching/moving molecule number 160 to 159 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 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_paule_data_greg-data_pdb1hvv.ent_Wed_Sep_19_11:45:45_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal 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) chain_id A master B rtop: [[0.3394591924816796, 0.5177117455596953, 0.7853292336015637, 0.8624279581117553, 0.16197572619124062, -0.4795642617960695, -0.3754803239943135, 0.8400823844328328, -0.39150493439900846], [90.55110034747929, -91.12318261711249, -47.52179998745863]] INFO:: Matching/moving molecule number 160 to 159 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.1943 rms devi: 0.2112 max devi: 0.3583 min devi: 0.0329 INFO:: Axis orientation: ( 0.1978, -0.3281, 0.9237) INFO:: Rotation in CCP4 Polar Angles: Polar = (22.5246,-58.9204,174.877) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Wed_Sep_19_11:45:45_2018_modification_1.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.9179, -0.212, 0.3353| | -0.04702, -0.7812, -0.6226| | 0.3939, -0.5873, 0.7071| ( 57.6, -116.4, -53.95) INFO:: fractional coordinates matrix: | -0.9451, -0.1016, -0.03159| | -0.05429, -0.754, -0.9411| | 0.3009, -0.5389, 0.7071| ( -0.109, -1.522, -0.4666) chain_id C master B rtop: [[-0.9179458350933407, -0.21199297393104302, 0.33531242571467806, -0.04701514428682865, -0.7811500284294697, -0.6225706460252742, 0.39390991361284383, -0.5872508936464131, 0.7070865349227144], [57.59590387868751, -116.43599115338534, -53.953192756327674]] INFO:: Matching/moving molecule number 160 to 159 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.4174 rms devi: 0.4531 max devi: 0.7926 min devi: 0.0759 INFO:: Axis orientation: ( 0.7055, 0.6938, 0.1447) INFO:: Rotation in CCP4 Polar Angles: Polar = (98.3189,-135.478,101.097) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Wed_Sep_19_11:45:45_2018_modification_2.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.401, 0.7256, -0.5591| | 0.4417, 0.3815, 0.812| | 0.8025, -0.5726, -0.1675| ( 8.426, 15.74, -123.4) INFO:: fractional coordinates matrix: | 0.656, 0.4912, -0.1182| | 0.51, 0.1265, 1.227| | 0.6131, -0.6853, -0.1675| ( 0.1983, 0.2058, -1.067) chain_id D master B rtop: [[0.4010296958260637, 0.7256475124974693, -0.5591161513244722, 0.44169126456601965, 0.38154476969746226, 0.8119928666697639, 0.8025484470558306, -0.5725899722513011, -0.16750138448839502], [8.42628578842055, 15.739925910905619, -123.41057067974724]] INFO:: Command: (close-molecule 160) NCS ghost chain IDs pre: [['B', 'A', 'C', 'D']] NCS ghost chain IDs post: [['B', 'A', 'C', 'D']] ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... INFO:: Command: (molecule-name 0) INFO:: Command: (molecule-name 1) INFO:: Command: (molecule-name 2) INFO:: Command: (molecule-name 3) INFO:: Command: (molecule-name 6) INFO:: Command: (molecule-name 7) INFO:: Command: (molecule-name 8) INFO:: Command: (molecule-name 9) INFO:: Command: (molecule-name 10) INFO:: Command: (molecule-name 11) INFO:: Command: (molecule-name 12) INFO:: Command: (molecule-name 14) INFO:: Command: (molecule-name 15) INFO:: Command: (molecule-name 17) INFO:: Command: (molecule-name 18) INFO:: Command: (molecule-name 19) INFO:: Command: (molecule-name 21) INFO:: Command: (molecule-name 22) INFO:: Command: (molecule-name 25) INFO:: Command: (molecule-name 26) INFO:: Command: (molecule-name 29) INFO:: Command: (molecule-name 31) INFO:: Command: (molecule-name 32) INFO:: Command: (molecule-name 34) INFO:: Command: (molecule-name 35) INFO:: Command: (molecule-name 36) INFO:: Command: (molecule-name 37) INFO:: Command: (molecule-name 39) INFO:: Command: (molecule-name 40) INFO:: Command: (molecule-name 41) INFO:: Command: (molecule-name 42) INFO:: Command: (molecule-name 43) INFO:: Command: (molecule-name 46) INFO:: Command: (molecule-name 55) INFO:: Command: (molecule-name 56) INFO:: Command: (molecule-name 58) INFO:: Command: (molecule-name 59) INFO:: Command: (molecule-name 60) INFO:: Command: (molecule-name 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 63) INFO:: Command: (molecule-name 64) INFO:: Command: (molecule-name 65) INFO:: Command: (molecule-name 66) INFO:: Command: (molecule-name 67) INFO:: Command: (molecule-name 68) INFO:: Command: (molecule-name 69) INFO:: Command: (molecule-name 70) INFO:: Command: (molecule-name 71) INFO:: Command: (molecule-name 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 75) INFO:: Command: (molecule-name 76) INFO:: Command: (molecule-name 77) INFO:: Command: (molecule-name 78) INFO:: Command: (molecule-name 79) INFO:: Command: (molecule-name 80) INFO:: Command: (molecule-name 81) INFO:: Command: (molecule-name 82) INFO:: Command: (molecule-name 83) INFO:: Command: (molecule-name 85) INFO:: Command: (molecule-name 86) INFO:: Command: (molecule-name 87) INFO:: Command: (molecule-name 88) INFO:: Command: (molecule-name 89) INFO:: Command: (molecule-name 90) INFO:: Command: (molecule-name 91) INFO:: Command: (molecule-name 92) INFO:: Command: (molecule-name 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 95) INFO:: Command: (molecule-name 96) INFO:: Command: (molecule-name 97) INFO:: Command: (molecule-name 98) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 100) INFO:: Command: (molecule-name 101) INFO:: Command: (molecule-name 103) INFO:: Command: (molecule-name 104) INFO:: Command: (molecule-name 105) INFO:: Command: (molecule-name 109) INFO:: Command: (molecule-name 110) INFO:: Command: (molecule-name 112) INFO:: Command: (molecule-name 113) INFO:: Command: (molecule-name 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 116) INFO:: Command: (molecule-name 117) INFO:: Command: (molecule-name 118) INFO:: Command: (molecule-name 119) INFO:: Command: (molecule-name 120) INFO:: Command: (molecule-name 121) INFO:: Command: (molecule-name 122) INFO:: Command: (molecule-name 123) INFO:: Command: (molecule-name 124) INFO:: Command: (molecule-name 125) INFO:: Command: (molecule-name 126) INFO:: Command: (molecule-name 130) INFO:: Command: (molecule-name 131) INFO:: Command: (molecule-name 132) INFO:: Command: (molecule-name 133) INFO:: Command: (molecule-name 134) INFO:: Command: (molecule-name 135) INFO:: Command: (molecule-name 136) INFO:: Command: (molecule-name 137) INFO:: Command: (molecule-name 138) INFO:: Command: (molecule-name 139) INFO:: Command: (molecule-name 140) INFO:: Command: (molecule-name 141) INFO:: Command: (molecule-name 142) INFO:: Command: (molecule-name 144) INFO:: Command: (molecule-name 145) INFO:: Command: (molecule-name 146) INFO:: Command: (molecule-name 147) INFO:: Command: (molecule-name 148) INFO:: Command: (molecule-name 149) INFO:: Command: (molecule-name 150) INFO:: Command: (close-molecule 152) INFO:: Command: (close-molecule 154) INFO:: Command: (molecule-name 156) INFO:: Command: (molecule-name 157) INFO:: Command: (molecule-name 158) INFO:: Command: (molecule-name 159) INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices 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 161 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/1hvv_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/1hvv_sigmaa.mtz Number of OBSERVED reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.0360 seconds to read MTZ file INFO:: 0.0210 seconds to initialize map INFO:: 0.0340 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0000 seconds for contour map INFO:: 0.0940 seconds in total INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.4989 rms devi: 2.7962 max devi: 6.6860 min devi: 0.4401 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: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.9713 rms devi: 2.1729 max devi: 4.5411 min devi: 0.4295 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: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.7042 rms devi: 4.0859 max devi: 9.4383 min devi: 0.2858 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 162 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 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 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 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 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 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 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: Command: (molecule-name 0) INFO:: Command: (molecule-name 1) INFO:: Command: (molecule-name 2) INFO:: Command: (molecule-name 3) INFO:: Command: (molecule-name 6) INFO:: Command: (molecule-name 7) INFO:: Command: (molecule-name 8) INFO:: Command: (molecule-name 9) INFO:: Command: (molecule-name 10) INFO:: Command: (molecule-name 11) INFO:: Command: (molecule-name 12) INFO:: Command: (molecule-name 14) INFO:: Command: (molecule-name 15) INFO:: Command: (molecule-name 17) INFO:: Command: (molecule-name 18) INFO:: Command: (molecule-name 19) INFO:: Command: (molecule-name 21) INFO:: Command: (molecule-name 22) INFO:: Command: (molecule-name 25) INFO:: Command: (molecule-name 26) INFO:: Command: (molecule-name 29) INFO:: Command: (molecule-name 31) INFO:: Command: (molecule-name 32) INFO:: Command: (molecule-name 34) INFO:: Command: (molecule-name 35) INFO:: Command: (molecule-name 36) INFO:: Command: (molecule-name 37) INFO:: Command: (molecule-name 39) INFO:: Command: (molecule-name 40) INFO:: Command: (molecule-name 41) INFO:: Command: (molecule-name 42) INFO:: Command: (molecule-name 43) INFO:: Command: (molecule-name 46) INFO:: Command: (molecule-name 55) INFO:: Command: (molecule-name 56) INFO:: Command: (molecule-name 58) INFO:: Command: (molecule-name 59) INFO:: Command: (molecule-name 60) INFO:: Command: (molecule-name 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 63) INFO:: Command: (molecule-name 64) INFO:: Command: (molecule-name 65) INFO:: Command: (molecule-name 66) INFO:: Command: (molecule-name 67) INFO:: Command: (molecule-name 68) INFO:: Command: (molecule-name 69) INFO:: Command: (molecule-name 70) INFO:: Command: (molecule-name 71) INFO:: Command: (molecule-name 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 75) INFO:: Command: (molecule-name 76) INFO:: Command: (molecule-name 77) INFO:: Command: (molecule-name 78) INFO:: Command: (molecule-name 79) INFO:: Command: (molecule-name 80) INFO:: Command: (molecule-name 81) INFO:: Command: (molecule-name 82) INFO:: Command: (molecule-name 83) INFO:: Command: (molecule-name 85) INFO:: Command: (molecule-name 86) INFO:: Command: (molecule-name 87) INFO:: Command: (molecule-name 88) INFO:: Command: (molecule-name 89) INFO:: Command: (molecule-name 90) INFO:: Command: (molecule-name 91) INFO:: Command: (molecule-name 92) INFO:: Command: (molecule-name 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 95) INFO:: Command: (molecule-name 96) INFO:: Command: (molecule-name 97) INFO:: Command: (molecule-name 98) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 100) INFO:: Command: (molecule-name 101) INFO:: Command: (molecule-name 103) INFO:: Command: (molecule-name 104) INFO:: Command: (molecule-name 105) INFO:: Command: (molecule-name 109) INFO:: Command: (molecule-name 110) INFO:: Command: (molecule-name 112) INFO:: Command: (molecule-name 113) INFO:: Command: (molecule-name 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 116) INFO:: Command: (molecule-name 117) INFO:: Command: (molecule-name 118) INFO:: Command: (molecule-name 119) INFO:: Command: (molecule-name 120) INFO:: Command: (molecule-name 121) INFO:: Command: (molecule-name 122) INFO:: Command: (molecule-name 123) INFO:: Command: (molecule-name 124) INFO:: Command: (molecule-name 125) INFO:: Command: (molecule-name 126) INFO:: Command: (molecule-name 130) INFO:: Command: (molecule-name 131) INFO:: Command: (molecule-name 132) INFO:: Command: (molecule-name 133) INFO:: Command: (molecule-name 134) INFO:: Command: (molecule-name 135) INFO:: Command: (molecule-name 136) INFO:: Command: (molecule-name 137) INFO:: Command: (molecule-name 138) INFO:: Command: (molecule-name 139) INFO:: Command: (molecule-name 140) INFO:: Command: (molecule-name 141) INFO:: Command: (molecule-name 142) INFO:: Command: (molecule-name 144) INFO:: Command: (molecule-name 145) INFO:: Command: (molecule-name 146) INFO:: Command: (molecule-name 147) INFO:: Command: (molecule-name 148) INFO:: Command: (molecule-name 149) INFO:: Command: (molecule-name 150) INFO:: Command: (molecule-name 156) INFO:: Command: (molecule-name 157) INFO:: Command: (molecule-name 158) INFO:: Command: (molecule-name 159) INFO:: Command: (molecule-name 161) BL DEBUG:: molecule_names ['/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/ins-code-fragment-pre.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', 'PTR_from_dict', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-modern.pdb', 'mainchain-forward', '/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb', 'regression-test-terminal-residue.pdb', 'atom selection from regression-test-terminal-residue.pdb', '/home/paule/data/greg-data/frag-2wot.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'sphere selection from tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rotamer-test-fragment.pdb', '/home/paule/data/greg-data/res098.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/pdb3knw.ent', '/home/paule/data/greg-data/pdb1py3.ent', '/home/paule/data/greg-data/alt-conf-pepflip-test.pdb', '/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/alt-conf-waters.pdb', '/home/paule/data/greg-data/backrub-fragment.pdb', 'Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT', '/home/paule/data/greg-data/test-TER-OXT.pdb', '/home/paule/data/greg-data/val.pdb', '/home/paule/data/greg-data/2yie-frag.pdb', '/home/paule/data/greg-data/4f8g.pdb', '/home/paule/data/greg-data/4f8g.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-modern.pdb', 'Generic Masked Map', 'difference-map', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'averaged-map', 'difference-map', '/home/paule/data/greg-data/multi-carbo-coot-3.pdb', '/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/monomer-VAL.pdb', '/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb', 'atom selection from tutorial-modern.pdb', '/home/paule/data/greg-data/monomer-ACT.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', 'atom selection from tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb3hfl.ent', '/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Ideal-A-form-RNA', 'Ideal-A-form-RNA', 'Ideal-A-form-DNA', 'Ideal-A-form-DNA', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/some-waters-with-ter.pdb', '/home/paule/data/greg-data/tm+some-waters.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/water-test-no-cell.pdb', '/home/paule/data/greg-data/pathological-water-test.pdb', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb1hvv.ent', '/home/paule/data/greg-data/monomer-ACT.pdb', '/home/paule/data/greg-data/monomer-NPO.pdb', 'SymOp_-X,-X+Y,-Z+1/3_Copy_of_87', '/home/paule/data/greg-data/tutorial-modern.pdb', 'atom selection from tutorial-modern.pdb', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb1py3.ent', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/2goz-manip.pdb', 'rnase_zip_test.pdb.gz', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/HOF.RES', '/home/paule/data/greg-data/hollander.ins', '/home/paule/data/greg-data/insulin.fcf Diff-SigmaA', 'atom selection from insulin.res', 'atom selection from insulin.res', '/home/paule/data/greg-data/horma-p21.res', 'new-horma.ins', '/home/paule/data/greg-data/crash.hat', '/home/paule/data/greg-data/crash.hat', 'coot-ccp4/monomer-3GP.pdb', '/home/paule/data/greg-data/monomer-3GP.pdb', '/home/paule/data/greg-data/test-LIG.pdb', '/home/paule/data/greg-data/test-LIG.pdb', '/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', '/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb', '/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT', '/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT', 'Masked (by protein)', 'Fitted ligand #0-0', 'Fitted ligand #1-0', 'Fitted ligand #2-0', 'Fitted ligand #3-0', 'Fitted ligand #4-0', 'Fitted ligand #5-0', 'Fitted ligand #6-0', 'Fitted ligand #7-0', 'Fitted ligand #8-0', 'Fitted ligand #9-0', '/home/paule/data/greg-data/dipole-residues.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', '/home/paule/data/greg-data/1wly.pdb', '/home/paule/data/greg-data/1yb5.pdb', '/home/paule/data/greg-data/2qd9.pdb', '/home/paule/data/greg-data/2gtn.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Map 4 NCS average of Chain A type molecules', 'Map 151 NCS average of Chain A type molecules', '/home/paule/data/greg-data/insulin.res', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb1t6q.ent', '/home/paule/data/greg-data/pdb1hvv.ent', '/home/paule/data/greg-data/pdb1hvv.ent', '/home/paule/data/greg-data/1hvv_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Map 162 NCS found from matching Chain B onto Chain A', 'Map 162 NCS found from matching Chain C onto Chain A', 'Map 162 NCS found from matching Chain D onto Chain A', 'Map 162 NCS average of Chain A type molecules', 'Map 162 NCS found from matching Chain B onto Chain A', 'Map 162 NCS found from matching Chain C onto Chain A', 'Map 162 NCS found from matching Chain D onto Chain A', 'Map 162 NCS average of Chain A type molecules'] BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... INFO:: Command: (+ 2 4) INFO:: Command: (rotation-centre) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) BL DEBUG:: return scheme is [24.219083786010742, -41.04264831542969, -67.95923614501953] INFO:: Command: 2 ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... Entering test: kevin's torsion test PASS: kevin's torsion test Entering test: test_alt_conf_rotamers INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_alt_conf_rotamers Entering test: test_fragmemt_atom_selection INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 n_initial: 1465 n_1: 1401 n_2: 64 PASS: test_fragmemt_atom_selection Entering test: test_add_atom INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_add_atom Entering test: test dictionary partial charges INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NA.cif PASS: test dictionary partial charges Entering test: test segid exchange INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Test with a rogue segid INFO:: No consistent segids for residue 1 PASS: test segid exchange Entering test: test ligand from point There are 2 data in /home/paule/data/greg-data/libcheck_3GP-torsion-filtered.cif INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... non-H torsion: 0 [torsion-restraint: CONST_1 " O6 " " C6 " " C5 " " N7 " 0.0000 0.0000 0 CONST ] non-H torsion: 1 [torsion-restraint: CONST_2 " C6 " " C5 " " C4 " " N3 " 0.0000 0.0000 0 CONST ] non-H torsion: 2 [torsion-restraint: CONST_3 " C6 " " C5 " " C4 " " N9 " 180.0000 0.0000 0 CONST ] non-H torsion: 3 [torsion-restraint: CONST_4 " C5 " " C4 " " N3 " " C2 " 0.0000 0.0000 0 CONST ] non-H torsion: 4 [torsion-restraint: CONST_5 " C4 " " N3 " " C2 " " N1 " 0.0000 0.0000 0 CONST ] non-H torsion: 5 [torsion-restraint: var_1 " N3 " " C2 " " N2 " "HN21" 0.0000 20.0000 1] non-H torsion: 6 [torsion-restraint: CONST_6 " N3 " " C2 " " N1 " " C6 " 0.0000 0.0000 0 CONST ] non-H torsion: 7 [torsion-restraint: CONST_12 " N3 " " C2 " " N1 " " HN1" 180.0000 0.0000 0 CONST ] non-H torsion: 8 [torsion-restraint: CONST_7 " C6 " " C5 " " N7 " " C8 " 180.0000 0.0000 0 CONST ] non-H torsion: 9 [torsion-restraint: CONST_8 " C5 " " N7 " " C8 " " N9 " 0.0000 0.0000 0 CONST ] non-H torsion: 10 [torsion-restraint: CONST_9 " N7 " " C8 " " N9 " " C1*" 180.0000 0.0000 0 CONST ] non-H torsion: 11 [torsion-restraint: CONST_10 " N7 " " C8 " " N9 " " C4 " 0.0000 0.0000 0 CONST ] non-H torsion: 12 [torsion-restraint: var_2 " C8 " " N9 " " C1*" " C2*" -78.3750 20.0000 1] non-H torsion: 13 [torsion-restraint: CONST_var_3 " N9 " " C1*" " O4*" " C4*" -152.9040 20.0000 1 CONST ] non-H torsion: 14 [torsion-restraint: CONST_var_4 " C1*" " O4*" " C4*" " C5*" 124.2120 20.0000 1 CONST ] non-H torsion: 15 [torsion-restraint: CONST_var_5 " C1*" " O4*" " C4*" " C3*" -3.5110 20.0000 1 CONST ] non-H torsion: 16 [torsion-restraint: var_6 " O4*" " C4*" " C5*" " O5*" -61.6860 20.0000 3] non-H torsion: 17 [torsion-restraint: var_7 " C4*" " C5*" " O5*" "HO5*" 0.0000 20.0000 1] non-H torsion: 18 [torsion-restraint: CONST_var_8 " N9 " " C1*" " C2*" " C3*" 155.4840 20.0000 3 CONST ] non-H torsion: 19 [torsion-restraint: CONST_var_9 " C1*" " C2*" " O2*" "HO2*" 0.0000 20.0000 1 CONST ] non-H torsion: 20 [torsion-restraint: CONST_var_10 " C1*" " C2*" " C3*" " O3*" 82.0740 20.0000 3 CONST ] non-H torsion: 21 [torsion-restraint: CONST_11 " C1*" " C2*" " C3*" " H3*" -157.9260 0.0000 0 CONST ] non-H torsion: 22 [torsion-restraint: CONST_var_11 " C1*" " C2*" " C3*" " C4*" -36.8410 20.0000 3 CONST ] non-H torsion: 23 [torsion-restraint: var_12 " C2*" " C3*" " O3*" " P " -179.7030 20.0000 1] non-H torsion: 24 [torsion-restraint: var_13 " C3*" " O3*" " P " " O2P" -156.9910 20.0000 1] non-H-non-ring-non-const torsion: 0 [torsion-restraint: var_1 " N3 " " C2 " " N2 " "HN21" 0.0000 20.0000 1] non-H-non-ring-non-const torsion: 1 [torsion-restraint: var_2 " C8 " " N9 " " C1*" " C2*" -78.3750 20.0000 1] non-H-non-ring-non-const torsion: 2 [torsion-restraint: var_6 " O4*" " C4*" " C5*" " O5*" -61.6860 20.0000 3] non-H-non-ring-non-const torsion: 3 [torsion-restraint: var_7 " C4*" " C5*" " O5*" "HO5*" 0.0000 20.0000 1] non-H-non-ring-non-const torsion: 4 [torsion-restraint: var_12 " C2*" " C3*" " O3*" " P " -179.7030 20.0000 1] non-H-non-ring-non-const torsion: 5 [torsion-restraint: var_13 " C3*" " O3*" " P " " O2P" -156.9910 20.0000 1] non-const-non-ring-tors: 0 [torsion-restraint: var_1 " N3 " " C2 " " N2 " "HN21" 0.0000 20.0000 1] -4.9673 non-const-non-ring-tors: 1 [torsion-restraint: var_2 " C8 " " N9 " " C1*" " C2*" -78.3750 20.0000 1] -74.5868 non-const-non-ring-tors: 2 [torsion-restraint: var_6 " O4*" " C4*" " C5*" " O5*" -61.6860 20.0000 3] 58.2464 non-const-non-ring-tors: 3 [torsion-restraint: var_7 " C4*" " C5*" " O5*" "HO5*" 0.0000 20.0000 1] -16.7803 non-const-non-ring-tors: 4 [torsion-restraint: var_12 " C2*" " C3*" " O3*" " P " -179.7030 20.0000 1] -169.9898 non-const-non-ring-tors: 5 [torsion-restraint: var_13 " C3*" " O3*" " P " " O2P" -156.9910 20.0000 1] -165.2413 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 379 non-bonded restraints initial distortion_score: 22.6850 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0274 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 476) at 11.0972 Final Estimated RMS Z Scores: bonds: 0.0858 angles: 0.4032 torsions: N/A planes: 0.0029 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 31.8588 90.0948 422.8129 ligand eigen vectors: | -0.07839, 0.212, -0.9741| | -0.3079, 0.9242, 0.226| | 0.9482, 0.3176, -0.007171| non-const-non-ring-tors: 0 [torsion-restraint: var_1 " N3 " " C2 " " N2 " "HN21" 0.0000 20.0000 1] 19.4140 non-const-non-ring-tors: 1 [torsion-restraint: var_2 " C8 " " N9 " " C1*" " C2*" -78.3750 20.0000 1] -76.1504 non-const-non-ring-tors: 2 [torsion-restraint: var_6 " O4*" " C4*" " C5*" " O5*" -61.6860 20.0000 3] 161.1230 non-const-non-ring-tors: 3 [torsion-restraint: var_7 " C4*" " C5*" " O5*" "HO5*" 0.0000 20.0000 1] -17.0255 non-const-non-ring-tors: 4 [torsion-restraint: var_12 " C2*" " C3*" " O3*" " P " -179.7030 20.0000 1] -177.7483 non-const-non-ring-tors: 5 [torsion-restraint: var_13 " C3*" " O3*" " P " " O2P" -156.9910 20.0000 1] -123.4053 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 378 non-bonded restraints initial distortion_score: 122.1803 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.2907 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 384) at 10.9763 Final Estimated RMS Z Scores: bonds: 0.0842 angles: 0.4010 torsions: N/A planes: 0.0221 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 26.1004 86.4442 439.0372 ligand eigen vectors: | -0.09218, 0.2057, -0.9743| | -0.2632, 0.9386, 0.223| | 0.9603, 0.277, -0.03239| non-const-non-ring-tors: 0 [torsion-restraint: var_1 " N3 " " C2 " " N2 " "HN21" 0.0000 20.0000 1] -0.3967 non-const-non-ring-tors: 1 [torsion-restraint: var_2 " C8 " " N9 " " C1*" " C2*" -78.3750 20.0000 1] -76.6802 non-const-non-ring-tors: 2 [torsion-restraint: var_6 " O4*" " C4*" " C5*" " O5*" -61.6860 20.0000 3] -67.8029 non-const-non-ring-tors: 3 [torsion-restraint: var_7 " C4*" " C5*" " O5*" "HO5*" 0.0000 20.0000 1] -16.5244 non-const-non-ring-tors: 4 [torsion-restraint: var_12 " C2*" " C3*" " O3*" " P " -179.7030 20.0000 1] -164.8020 non-const-non-ring-tors: 5 [torsion-restraint: var_13 " C3*" " O3*" " P " " O2P" -156.9910 20.0000 1] -192.1895 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 385 non-bonded restraints initial distortion_score: 64.7042 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.1361 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 414) at 11.2215 Final Estimated RMS Z Scores: bonds: 0.0852 angles: 0.4057 torsions: N/A planes: 0.0069 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 25.2316 91.9037 418.2715 ligand eigen vectors: | -0.05974, 0.2104, -0.9758| | -0.1493, 0.9647, 0.2171| | 0.987, 0.1587, -0.02621| non-const-non-ring-tors: 0 [torsion-restraint: var_1 " N3 " " C2 " " N2 " "HN21" 0.0000 20.0000 1] -7.6632 non-const-non-ring-tors: 1 [torsion-restraint: var_2 " C8 " " N9 " " C1*" " C2*" -78.3750 20.0000 1] -63.0223 non-const-non-ring-tors: 2 [torsion-restraint: var_6 " O4*" " C4*" " C5*" " O5*" -61.6860 20.0000 3] -52.0592 non-const-non-ring-tors: 3 [torsion-restraint: var_7 " C4*" " C5*" " O5*" "HO5*" 0.0000 20.0000 1] -22.7073 non-const-non-ring-tors: 4 [torsion-restraint: var_12 " C2*" " C3*" " O3*" " P " -179.7030 20.0000 1] -203.2729 non-const-non-ring-tors: 5 [torsion-restraint: var_13 " C3*" " O3*" " P " " O2P" -156.9910 20.0000 1] -126.8868 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 381 non-bonded restraints initial distortion_score: 22.6852 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0273 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 352) at 10.8970 Final Estimated RMS Z Scores: bonds: 0.0831 angles: 0.3997 torsions: N/A planes: 0.0092 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 31.0896 84.1626 426.2558 ligand eigen vectors: | -0.1154, 0.2195, -0.9688| | -0.3215, 0.9145, 0.2455| | 0.9399, 0.3398, -0.035| non-const-non-ring-tors: 0 [torsion-restraint: var_1 " N3 " " C2 " " N2 " "HN21" 0.0000 20.0000 1] -6.5237 non-const-non-ring-tors: 1 [torsion-restraint: var_2 " C8 " " N9 " " C1*" " C2*" -78.3750 20.0000 1] -81.3838 non-const-non-ring-tors: 2 [torsion-restraint: var_6 " O4*" " C4*" " C5*" " O5*" -61.6860 20.0000 3] 193.5140 non-const-non-ring-tors: 3 [torsion-restraint: var_7 " C4*" " C5*" " O5*" "HO5*" 0.0000 20.0000 1] -41.4762 non-const-non-ring-tors: 4 [torsion-restraint: var_12 " C2*" " C3*" " O3*" " P " -179.7030 20.0000 1] -191.9713 non-const-non-ring-tors: 5 [torsion-restraint: var_13 " C3*" " O3*" " P " " O2P" -156.9910 20.0000 1] -168.8346 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 377 non-bonded restraints initial distortion_score: 22.6851 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0276 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 286) at 10.8336 Final Estimated RMS Z Scores: bonds: 0.0838 angles: 0.3983 torsions: N/A planes: 0.0332 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 22.7520 88.4663 441.0335 ligand eigen vectors: | -0.132, 0.1953, -0.9718| | -0.2313, 0.9473, 0.2218| | 0.9639, 0.2541, -0.0799| INFO:: Protein centre at: xyz = ( 41.53, 8.726, 12.87) There are 1 clusters Here are the top 10 clusters: Number: 0 # grid points: 264 score: 146.5952 | -0.1765, 0.981, -0.08001| | 0.2847, 0.1287, 0.9499| | 0.9422, 0.1449, -0.302| ( 55.49, 9.316, 20.62) xyz = ( 3.05, 1.281, 0.8881) eigenvalues: 131.0082 2545.3515 421.9402 found distance from reference centre 0.4247 PASS: test ligand from point Entering test: test peak search non-close reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... INFO:: peak filtering: npeaks: in: 5158 out: 2105 There are 2105 peaks and 0 problem peaks PASS: test peak search non-close Entering test: test symop card 1 0 0 0 1 0 0 0 1 translations: -1.0000 0.0000 0.0000 PASS: test symop card Entering test: test rotate round vector INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 0 O6 0.9397 -> 20.0000 degrees 1 C6 0.9397 -> 20.0000 degrees 2 C5 0.9397 -> 20.0000 degrees 3 C4 0.9397 -> 20.0000 degrees 4 N3 0.9397 -> 20.0000 degrees 5 C2 0.9397 -> 20.0000 degrees 6 N2 0.9397 -> 20.0000 degrees 7 HN22 0.9397 -> 20.0000 degrees 8 HN21 0.9397 -> 20.0000 degrees 9 N1 0.9397 -> 20.0000 degrees 10 HN1 0.9397 -> 20.0000 degrees 11 N7 0.9397 -> 20.0000 degrees 12 C8 0.9397 -> 20.0000 degrees 13 H8 0.9397 -> 20.0000 degrees 16 H1* 0.9397 -> 20.0000 degrees 17 O4* 0.9397 -> 20.0000 degrees 18 C4* 0.9397 -> 20.0000 degrees 19 H4* 0.9397 -> 20.0000 degrees 20 C5* 0.9397 -> 20.0000 degrees 21 H5*1 0.9397 -> 20.0000 degrees 22 H5*2 0.9397 -> 20.0000 degrees 23 O5* 0.9397 -> 20.0000 degrees 24 HO5* 0.9397 -> 20.0000 degrees 25 C2* 0.9397 -> 20.0000 degrees 26 H2* 0.9397 -> 20.0000 degrees 27 O2* 0.9397 -> 20.0000 degrees 28 HO2* 0.9397 -> 20.0000 degrees 29 C3* 0.9397 -> 20.0000 degrees 30 H3* 0.9397 -> 20.0000 degrees 31 O3* 0.9397 -> 20.0000 degrees 32 P 0.9397 -> 20.0000 degrees 33 O1P 0.9397 -> 20.0000 degrees 34 O3P 0.9397 -> 20.0000 degrees 35 O2P 0.9397 -> 20.0000 degrees PASS: test rotate round vector Entering test: SSM sequence alignment output -- Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC -- Moving: D Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG -- Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG -- PASS: SSM sequence alignment output ok ====================================================================== FAIL: test15_1 (__main__.PdbMtzTestFunctions) HIS with unusual atom order rotates correct fragment for 180 sidechain flip ---------------------------------------------------------------------- Traceback (most recent call last): File "python-tests/01_pdb_mtz.py", line 515, in test15_1 "BAD imol for 180 sidechain flip test imol: %s" %imol) AssertionError: BAD imol for 180 sidechain flip test imol: -1 ---------------------------------------------------------------------- Ran 129 tests in 39.147s FAILED (failures=1) test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... ok test05_1 (__main__.PdbMtzTestFunctions) Replace Residue gets correct residue number ... ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... ok test07_1 (__main__.PdbMtzTestFunctions) Auto-read bad MTZ test ... ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... ok test09_1 (__main__.PdbMtzTestFunctions) db-main makes mainchain ... ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... ok test11_2 (__main__.PdbMtzTestFunctions) Add Terminal Residue O Position ... ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... ok test15_1 (__main__.PdbMtzTestFunctions) HIS with unusual atom order rotates correct fragment for 180 sidechain flip ... FAIL test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... ok test16_3 (__main__.PdbMtzTestFunctions) Hs are correctly swapped on a TYR ... ok test16_4 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... ok test18_1 (__main__.PdbMtzTestFunctions) H on a N moves on cis-trans convert ... ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... ok test20_2 (__main__.PdbMtzTestFunctions) Neighbour-Refine doesn't destroy disulfide bonds ... ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... ok test29_1 (__main__.PdbMtzTestFunctions) Skeletonize a map ... ok test29_2 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... ok test30_1 (__main__.PdbMtzTestFunctions) Refine an NAG-ASN Link ... ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... ok test32_0 (__main__.PdbMtzTestFunctions) Test for regularization and mangling of hydrogen names from a PDB v 3.0 ... ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... ok test35_1 (__main__.PdbMtzTestFunctions) Chain-ids in links change also on change chain id ... ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... ok test52_2 (__main__.PdbMtzTestFunctions) Test for good chain ids after a merge ... ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... ok test60_0 (__main__.PdbMtzTestFunctions) post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok test61_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... ok test62_0 (__main__.PdbMtzTestFunctions) Fix for Oliver Clarke fit by atom selection bug ... ok test999_0 (__main__.PdbMtzTestFunctions) Renumber residue range without overwriting coordinates. ... ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... ok test08_0 (__main__.LigandTestFunctions) Test dipole ... ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... ok test10_0 (__main__.LigandTestFunctions) Pyrogen Runs OK? ... ok test11_0 (__main__.LigandTestFunctions) pyrogen dictionary does not make double-quoted atom names ... ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... ok ====================================================================== FAIL: test15_1 (__main__.PdbMtzTestFunctions) HIS with unusual atom order rotates correct fragment for 180 sidechain flip ---------------------------------------------------------------------- Traceback (most recent call last): File "python-tests/01_pdb_mtz.py", line 515, in test15_1 "BAD imol for 180 sidechain flip test imol: %s" %imol) AssertionError: BAD imol for 180 sidechain flip test imol: -1 ---------------------------------------------------------------------- Ran 129 tests in 39.147s FAILED (failures=1) Unitest skip does not exist! The following tests were skipped and marked as passed: Libcif horne Pyrogen Runs OK? pyrogen dictionary does not make double-quoted atom names INFO:: Command: (close-molecule 0) INFO:: Command: (close-molecule 1) INFO:: Command: (close-molecule 2) INFO:: Command: (close-molecule 3) INFO:: Command: (close-molecule 4) INFO:: Command: (close-molecule 5) INFO:: Command: (close-molecule 6) INFO:: Command: (close-molecule 7) INFO:: Command: (close-molecule 8) INFO:: Command: (close-molecule 9) INFO:: Command: (close-molecule 10) INFO:: Command: (close-molecule 11) INFO:: Command: (close-molecule 12) INFO:: Command: (close-molecule 13) INFO:: Command: (close-molecule 14) INFO:: Command: (close-molecule 15) INFO:: Command: (close-molecule 17) INFO:: Command: (close-molecule 18) INFO:: Command: (close-molecule 19) INFO:: Command: (close-molecule 20) INFO:: Command: (close-molecule 21) INFO:: Command: (close-molecule 22) INFO:: Command: (close-molecule 25) INFO:: Command: (close-molecule 26) INFO:: Command: (close-molecule 29) INFO:: Command: (close-molecule 30) INFO:: Command: (close-molecule 31) INFO:: Command: (close-molecule 32) INFO:: Command: (close-molecule 33) INFO:: Command: (close-molecule 34) INFO:: Command: (close-molecule 35) INFO:: Command: (close-molecule 36) INFO:: Command: (close-molecule 37) INFO:: Command: (close-molecule 38) INFO:: Command: (close-molecule 39) INFO:: Command: (close-molecule 40) INFO:: Command: (close-molecule 41) INFO:: Command: (close-molecule 42) INFO:: Command: (close-molecule 43) INFO:: Command: (close-molecule 44) INFO:: Command: (close-molecule 45) INFO:: Command: (close-molecule 46) INFO:: Command: (close-molecule 47) INFO:: Command: (close-molecule 48) INFO:: Command: (close-molecule 51) INFO:: Command: (close-molecule 52) INFO:: Command: (close-molecule 53) INFO:: Command: (close-molecule 54) INFO:: Command: (close-molecule 55) INFO:: Command: (close-molecule 56) INFO:: Command: (close-molecule 57) INFO:: Command: (close-molecule 58) INFO:: Command: (close-molecule 59) INFO:: Command: (close-molecule 60) INFO:: Command: (close-molecule 61) INFO:: Command: (close-molecule 62) INFO:: Command: (close-molecule 63) INFO:: Command: (close-molecule 64) INFO:: Command: (close-molecule 65) INFO:: Command: (close-molecule 66) INFO:: Command: (close-molecule 67) INFO:: Command: (close-molecule 68) INFO:: Command: (close-molecule 69) INFO:: Command: (close-molecule 70) INFO:: Command: (close-molecule 71) INFO:: Command: (close-molecule 72) INFO:: Command: (close-molecule 73) INFO:: Command: (close-molecule 74) INFO:: Command: (close-molecule 75) INFO:: Command: (close-molecule 76) INFO:: Command: (close-molecule 77) INFO:: Command: (close-molecule 78) INFO:: Command: (close-molecule 79) INFO:: Command: (close-molecule 80) INFO:: Command: (close-molecule 81) INFO:: Command: (close-molecule 82) INFO:: Command: (close-molecule 83) INFO:: Command: (close-molecule 84) INFO:: Command: (close-molecule 85) INFO:: Command: (close-molecule 86) INFO:: Command: (close-molecule 87) INFO:: Command: (close-molecule 88) INFO:: Command: (close-molecule 89) INFO:: Command: (close-molecule 90) INFO:: Command: (close-molecule 91) INFO:: Command: (close-molecule 92) INFO:: Command: (close-molecule 93) INFO:: Command: (close-molecule 94) INFO:: Command: (close-molecule 95) INFO:: Command: (close-molecule 96) INFO:: Command: (close-molecule 97) INFO:: Command: (close-molecule 98) INFO:: Command: (close-molecule 99) INFO:: Command: (close-molecule 100) INFO:: Command: (close-molecule 101) INFO:: Command: (close-molecule 102) INFO:: Command: (close-molecule 103) INFO:: Command: (close-molecule 104) INFO:: Command: (close-molecule 105) INFO:: Command: (close-molecule 108) INFO:: Command: (close-molecule 109) INFO:: Command: (close-molecule 110) INFO:: Command: (close-molecule 112) INFO:: Command: (close-molecule 113) INFO:: Command: (close-molecule 114) INFO:: Command: (close-molecule 115) INFO:: Command: (close-molecule 116) INFO:: Command: (close-molecule 117) INFO:: Command: (close-molecule 118) INFO:: Command: (close-molecule 119) INFO:: Command: (close-molecule 120) INFO:: Command: (close-molecule 121) INFO:: Command: (close-molecule 122) INFO:: Command: (close-molecule 123) INFO:: Command: (close-molecule 124) INFO:: Command: (close-molecule 125) INFO:: Command: (close-molecule 126) INFO:: Command: (close-molecule 127) INFO:: Command: (close-molecule 128) INFO:: Command: (close-molecule 129) INFO:: Command: (close-molecule 130) INFO:: Command: (close-molecule 131) INFO:: Command: (close-molecule 132) INFO:: Command: (close-molecule 133) INFO:: Command: (close-molecule 134) INFO:: Command: (close-molecule 135) INFO:: Command: (close-molecule 136) INFO:: Command: (close-molecule 137) INFO:: Command: (close-molecule 138) INFO:: Command: (close-molecule 139) INFO:: Command: (close-molecule 140) INFO:: Command: (close-molecule 141) INFO:: Command: (close-molecule 142) INFO:: Command: (close-molecule 143) INFO:: Command: (close-molecule 144) INFO:: Command: (close-molecule 145) INFO:: Command: (close-molecule 146) INFO:: Command: (close-molecule 147) INFO:: Command: (close-molecule 148) INFO:: Command: (close-molecule 149) INFO:: Command: (close-molecule 150) INFO:: Command: (close-molecule 151) INFO:: Command: (close-molecule 153) INFO:: Command: (close-molecule 155) INFO:: Command: (close-molecule 156) INFO:: Command: (close-molecule 157) INFO:: Command: (close-molecule 158) INFO:: Command: (close-molecule 159) INFO:: Command: (close-molecule 161) INFO:: Command: (close-molecule 162) INFO:: Command: (close-molecule 163) INFO:: Command: (close-molecule 164) INFO:: Command: (close-molecule 165) INFO:: Command: (close-molecule 166) INFO:: Command: (close-molecule 167) INFO:: Command: (close-molecule 168) INFO:: Command: (close-molecule 169) INFO:: Command: (close-molecule 170) gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable FINALLY collect some GARBAGE BL INFO:: no of collected carbage items 6 BL DEBUG:: list of garbage items: (, , ) Detailed information for functions: BL INFO:: garbage item and location: BL INFO:: garbage item and location: INFO:: Command: (use-graphics-interface-state) INFO:: Command: (stereo-mode-state) INFO:: Command: (stereo-mode-state) INFO:: Command: (save-state) Good morning root. Welcome to Coot 0.8.9.2-pre. ObjectCache: Leaked 0005 refs to

ObjectCache: Leaked 0004 refs to ObjectCache: Leaked 0005 refs to

ObjectCache: Leaked 0004 refs to Guile 1.8.8 Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation Guile may be distributed under the terms of the GNU General Public Licence; certain other uses are permitted as well. For details, see the file `COPYING', which is included in the Guile distribution. There is no warranty, to the extent permitted by law. catching the crash log: (coot-crash-catcher.scm:1489): Gtk-WARNING **: cannot open display: test_coot_python: coot test failed