testing with greg testing with greg currently we are here: /home/paule/autobuild/building/emsley-vm-ubuntu1404_2018-09-19__T10_36_02/coot-0.8.9.2-pre Wed Sep 19 11:44:24 BST 2018 WARNING:: ccp4 setup file setup-ccp4 does not exist. /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm 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 command-line-greg.scm 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 Molecule number -5 is not a valid model molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/2WF6.cif mmCIF file /home/paule/data/greg-data/2WF6.cif 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 1 read successfully DEBUG:: there were 3 types with no dictionary in new_molecule_by_atom_selection Something bad happened - No atoms selected 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 2 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Creating directory coot-backup INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Wed_Sep_19_11:44:32_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Wed_Sep_19_11:44:32_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Wed_Sep_19_11:44:32_2018_modification_2.pdb.gz 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 3 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:44:32_2018_modification_0.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:44:32_2018_modification_1.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:44:32_2018_modification_2.pdb.gz 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_11:44:32_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_11:44:32_2018_modification_4.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Wed_Sep_19_11:44:32_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_11:44:32_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:32_2018_modification_1.pdb.gz 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 123) at 55.41 Final Estimated RMS Z Scores: bonds: 0.41 angles: 1.25 torsions: N/A planes: 0.58 non-bonded: 0.00 chiral vol: 2.34 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_11:44:32_2018_modification_2.pdb.gz INFO:: replace_coords: 16 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it WARNING:: Error reading bogus.map Read map bogus.map failed WARNING:: Can't find file bogus.mtz 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:: 0.08 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz 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:: 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 1.80 INFO grid sampling...Nuvw = ( 80, 108, 108) 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: ....... 0.26 Map maximum: ..... 1.82 Map minimum: ..... -1.02 INFO:: 0.00 seconds for contour map INFO:: 0.06 seconds in total INFO:: map file type was determined to be CCP4 type INFO:: attempting to read CCP4 map: test-3hfl.map Map statistics: mean: 0.00 st.d: 0.26 Map statistics: min: -1.02, max: 1.82 -0.99 5 -0.92 16 -0.85 73 -0.77 214 -0.70 683 -0.63 1662 -0.56 3458 -0.49 6630 -0.42 10974 -0.35 16784 -0.28 24050 -0.21 35976 -0.14 52684 -0.06 70826 0.01 75511 0.08 59049 0.15 33738 0.22 17844 0.29 11108 0.36 8875 0.43 7682 0.50 6862 0.58 5661 0.65 4738 0.72 3751 0.79 2781 0.86 1898 0.93 1313 1.00 799 1.07 428 1.14 224 1.21 120 1.29 55 1.36 44 1.43 20 1.50 9 1.57 7 1.64 4 1.71 3 1.78 1 1.85 0 INFO:: n grid points: 466560 INFO:: mean before filtering: 0.00 INFO:: variance before filtering: 0.07 INFO:: filter by ignoring 364 of 466560 counts ( = 0.0780%) with values around -0.0343 from bin 3480 of 10000 Map mean: ........ 0.0000 Map rmsd: ........ 0.2605 Map maximum: ..... 1.8188 Map minimum: ..... -1.0235 WARNING:: Error reading . . is a directory. 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 9 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:: 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 11 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_11:44:34_2018_modification_0.pdb.gz not backwards A contains 114 residues from -19 to 93 target fragment start res: -19 had 0 db fragment hits, ilength=6 retrying with ilength = 5 produces 14 hits. 2nd part with ilength = 5, iresno=-18 produces 9 hits. target fragment start res: -16 had 22 db fragment hits, ilength=6 target fragment start res: -13 had 48 db fragment hits, ilength=6 target fragment start res: -10 had 29 db fragment hits, ilength=6 target fragment start res: -7 had 1772 db fragment hits, ilength=6 target fragment start res: -4 had 2040 db fragment hits, ilength=6 target fragment start res: -1 had 2021 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 2 merge fragments -19 to 6 with 8 fit sets to merge The merging is complete mainchain_fragment from -19 to 6 done mainchain_fragment successfully set cell and symmetry short target_ca 0 with iresno 10, trying 9 short target_ca 0 with iresno 9, trying 8 WARNING:: short target at start - bailing out now. merge fragments 10 to 30 with 0 fit sets to merge The merging is complete mainchain_fragment from 10 to 30 done mainchain_fragment (process:423): Gtk-CRITICAL **: IA__gtk_widget_show: assertion 'GTK_IS_WIDGET (widget)' failed 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 13 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_11:44:35_2018_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Wed_Sep_19_11:44:35_2018_modification_0.pdb.gz 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 15 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 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 16 read successfully DEBUG:: there were 0 types with no dictionary 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0290 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0250 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0590 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/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:35_2018_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:35_2018_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:35_2018_modification_2.pdb.gz 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 20 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 ""] WARNING:: Error reading /home/paule/data/greg-data/eleanor-HIS.pdb 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 21 read successfully DEBUG:: there were 0 types with no dictionary 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: 599.3325 Initial RMS Z values bonds: 0.1989 angles: 0.4071 torsions: N/A planes: 0.5035 non-bonded: 4.4321 chiral vol: 0.1627 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 239) at 9.9937 Final Estimated RMS Z Scores: bonds: 0.0729 angles: 0.6197 torsions: N/A planes: 0.5967 non-bonded: 0.0000 chiral vol: 0.5924 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.6490 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Wed_Sep_19_11:44:36_2018_modification_0.pdb.gz INFO:: replace_coords: 11 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 22 read successfully DEBUG:: there were 0 types with no dictionary 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0290 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0250 seconds for FFT INFO:: 0.0040 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0600 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_11:44:36_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:423): 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_11:44:36_2018_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.9313 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 24 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_11:44:36_2018_modification_0.pdb.gz Good morning root. Welcome to Coot 0.8.9.2-pre. === greg-tests tests === Loading greg-tests/begin.grg ... =============================================================== ==================== Testing ================================== =============================================================== Loaded greg-tests/begin.grg Running 01-pdb+mtz.scm ... Entered testcase - Post Go To Atom no molecules PASS: Post Go To Atom no molecules Entered testcase - Close bad molecule PASS: Close bad molecule Entered testcase - Read coordinates test PASS: Read coordinates test Entered testcase - New molecule from bogus molecule PASS: New molecule from bogus molecule Entered testcase - Don't crash on empty NCS from mmCIF file closing molecule number 1 PASS: Don't crash on empty NCS from mmCIF file Entered testcase - New molecule from bogus atom selection INFO:: pre-n-molecules 2 post-n-molecules 2 PASS: New molecule from bogus atom selection Entered testcase - ins code change and Goto atom over an ins code break pre and post ins codes: "" "A" pass: ("A" 68 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "A" " CA ") pass: ("A" 68 "" " CA ") pass: ("A" 66 "" " CA ") PASS: ins code change and Goto atom over an ins code break Entered testcase - Replace Residue gets correct residue number new-chain-id-info: (1 ((#t "A" 101 ""))) debug:: new-res-spec: (#t "A" 101 "") debug:: change-residue-number to 86 C-N dist good enough: 1.33561583204041 PASS: Replace Residue gets correct residue number Entered testcase - Read a bogus map PASS: Read a bogus map Entered testcase - Read MTZ test PASS: Read MTZ test Entered testcase - Auto-read bad MTZ test got status: #() got status: #() PASS: Auto-read bad MTZ test Entered testcase - Map Sigma INFO:: map sigmas 0.311501026153564 #f PASS: Map Sigma Entered testcase - Another Level Test PASS: Another Level Test Entered testcase - Sharpen map from map PASS: Sharpen map from map Entered testcase - db-main makes mainchain PASS: db-main makes mainchain Entered testcase - Negative Residues in db-mainchain don't cause a crash PASS: Negative Residues in db-mainchain don't cause a crash Entered testcase - Set Atom Attribute Test PASS: Set Atom Attribute Test Entered testcase - Add Terminal Residue Test PASS: Add Terminal Residue Test Entered testcase - Adding residue by phi psi, no crash PASS: Adding residue by phi psi, no crash Entered testcase - Add Terminal Residue O Position Add terminal residue bond check dd-1: 0.14997610541894 Add terminal residue bond check dd-2: 2.25586252670689 PASS: Add Terminal Residue O Position Entered testcase - Select by Sphere Sphere mol: there are 4 residues in chain "B" Found 20 sphere atoms PASS: Select by Sphere Entered testcase - Test Views PASS: Test Views Entered testcase - Label Atoms and Delete PASS: Label Atoms and Delete Entered testcase - Rotamer outliers PASS: Rotamer outliers Entered testcase - HIS with unusual atom order rotates correct fragment for 180 sidechain flip BAD imol for 180 sidechain flip test imol: -1 FAIL: HIS with unusual atom order rotates correct fragment for 180 sidechain flip Entered testcase - Alt Conf Occ Sum Reset For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 PASS: Alt Conf Occ Sum Reset Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue PASS: Correct occupancies after auto-fit rotamer on alt-confed residue Entered testcase - Rotamers work on MSE se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983INFO:: 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 25 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_11:44:36_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 906746)) se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616)) PASS: Rotamers work on MSE Entered testcase - Hs are correctly swapped on a TYR bond-length-within-tolerance? bond-length 0.93069991132425 with target 0.93 and tolerance 0.02 for atom ((" CD1" "") (1.0 (22.3700008392334 0.288300007581711 0.351099997758865 0.210400000214577 0.0551000013947487 0.0124000003561378 0.00350000010803342) " C" "") (61.2610015869141 -13.2200002670288 1.25)) is ((" HD1" "") (1.0 22.7800006866455 " H" "") (61.4099998474121 -12.8690004348755 2.09899997711182)) bond-length-within-tolerance? bond-length 0.930136198469449 with target 0.93 and tolerance 0.02 for atom ((" CD2" "") (1.0 (24.4099998474121 0.258899986743927 0.405699998140335 0.262800008058548 0.0627999976277351 -0.0269000008702278 -0.00970000028610229) " C" "") (59.9500007629395 -13.3459997177124 -0.740000009536743)) is ((" HD2" "") (1.0 24.3099994659424 " H" "") (59.2050018310547 -13.0869998931885 -1.23300004005432)) bond-length-within-tolerance? bond-length 0.930888837109095 with target 0.93 and tolerance 0.02 for atom ((" CE1" "") (1.0 (22.1599998474121 0.280600011348724 0.314999997615814 0.246199995279312 0.0603000000119209 -0.0186000000685453 -0.0172000005841255) " C" "") (62.1650009155273 -14.1079998016357 0.726000010967255)) is ((" HE1" "") (1.0 22.1200008392334 " H" "") (62.9140014648438 -14.3520002365112 1.22200000286102)) bond-length-within-tolerance? bond-length 0.929591631283786 with target 0.93 and tolerance 0.02 for atom ((" CE2" "") (1.0 (23.9099998474121 0.281399995088577 0.359200000762939 0.267500013113022 0.0529999993741512 -0.0285000000149012 -0.0131999999284744) " C" "") (60.8559989929199 -14.2670001983643 -1.29900002479553)) is ((" HE2" "") (1.0 23.5400009155273 " H" "") (60.7249984741211 -14.6049995422363 -2.15499997138977)) INFO:: 25 residues had their atoms swapped 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 26 read successfully DEBUG:: there were 0 types with no dictionary 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0290 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0620 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_11:44:36_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" 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 28 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_11:44:36_2018_modification_0.pdb.gz 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 29 read successfully DEBUG:: there were 0 types with no dictionary omega: 1 12.7704 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_11:44:37_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_11:44:37_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_11:44:37_2018_modification_2.pdb.gz 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: 4729.1878 Initial RMS Z values bonds: 15.4585 angles: 7.1242 torsions: N/A planes: 1.8999 non-bonded: 29.0131 chiral vol: 3.0446 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 106) at -4887.2387 Final Estimated RMS Z Scores: bonds: 0.8690 angles: 0.7626 torsions: N/A planes: 2.2102 non-bonded: 0.0646 chiral vol: 0.3524 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.3860 Refinement elapsed time: 0.0110 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:44:37_2018_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. (process:423): 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_11:44:37_2018_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:44:37_2018_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.6842 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: -6033.2814 Initial RMS Z values bonds: 0.8925 angles: 1.5991 torsions: N/A planes: 2.6482 non-bonded: 0.2248 chiral vol: 0.4011 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -6162.1606 Final Estimated RMS Z Scores: bonds: 0.8573 angles: 0.7010 torsions: N/A planes: 2.2620 non-bonded: 0.0430 chiral vol: 0.2062 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.4750 Refinement elapsed time: 0.0120 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Sep_19_11:44:37_2018_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 30 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:37_2018_modification_0.pdb.gz cliquize 12 spinables for altconf --------------------------- 12 cliques ---------------- omega: 1 -177.7480 degrees INFO This is a TRANS peptide - making it CIS 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:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:37_2018_modification_0.pdb.gz cliquize 11 spinables for altconf --------------------------- 10 cliques ---------------- 3 --- [spec: model 1 "A" 6 "" " CG1" ""] [spec: model 1 "A" 11 "" " CD2" ""] INFO:: mutate 10 A to a GLY INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:37_2018_modification_1.pdb.gz 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:: 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0260 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0590 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: -3224.8405 Initial RMS Z values bonds: 2.0711 angles: 1.0696 torsions: N/A planes: 0.6113 non-bonded: 3.4160 chiral vol: 1.4620 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 75) at -3460.9490 Final Estimated RMS Z Scores: bonds: 1.0098 angles: 1.3145 torsions: N/A planes: 0.2374 non-bonded: 0.3146 chiral vol: 1.2309 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.7090 Refinement elapsed time: 0.0060 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:37_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 36 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_11:44:37_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" 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 3.4824 FAIL close enough with closer than dist_crit 3.4824 FAIL close enough with closer than dist_crit 3.4824 FAIL close enough with closer than dist_crit 3.4824 FAIL close enough with closer than dist_crit 3.5194 FAIL close enough with closer than dist_crit 3.5194 FAIL close enough with closer than dist_crit 3.5194 FAIL close enough with closer than dist_crit 3.5194 FAIL close enough with closer than dist_crit 3.9048 FAIL close enough with closer than dist_crit 3.9048 FAIL close enough with closer than dist_crit 3.9048 FAIL close enough with closer than dist_crit 3.9048 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: -15829.7351 Initial RMS Z values bonds: 1.7426 angles: 1.2676 torsions: N/A planes: 0.8383 non-bonded: 0.0007 chiral vol: 0.8944 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -16198.2121 Final Estimated RMS Z Scores: bonds: 0.9281 angles: 0.6210 torsions: N/A planes: 0.5922 non-bonded: 0.0000 chiral vol: 0.2845 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.8120 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Sep_19_11:44:37_2018_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 3.2722 FAIL close enough with closer than dist_crit 3.2722 FAIL close enough with closer than dist_crit 3.2722 FAIL close enough with closer than dist_crit 3.2722 FAIL close enough with closer than dist_crit 3.3704 FAIL close enough with closer than dist_crit 3.3704 FAIL close enough with closer than dist_crit 3.3704 FAIL close enough with closer than dist_crit 3.3704 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 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: -7315.0532 Initial RMS Z values bonds: 0.9807 angles: 1.0175 torsions: N/A planes: 1.7875 non-bonded: 5.2955 chiral vol: 10.2816 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -15843.9079 Final Estimated RMS Z Scores: bonds: 1.9850 angles: 1.8676 torsions: N/A planes: 1.5650 non-bonded: 0.0542 chiral vol: 1.8185 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.9210 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Sep_19_11:44:37_2018_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 37 read successfully DEBUG:: there were 0 types with no dictionary 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0260 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0580 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 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 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: -3137.5312 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 35) at -11537.1384 Final Estimated RMS Z Scores: bonds: 2.0176 angles: 2.0470 torsions: N/A planes: 1.6905 non-bonded: 0.0661 chiral vol: 2.0989 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.1060 Refinement elapsed time: 0.0550 ---------------------------------------------- ---------------------------------------------- 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 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 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: 4890.2353 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 69) at -2814.0095 Final Estimated RMS Z Scores: bonds: 0.7847 angles: 1.3972 torsions: N/A planes: 1.8339 non-bonded: 0.0187 chiral vol: 1.2442 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.2690 Refinement elapsed time: 0.1630 ---------------------------------------------- ---------------------------------------------- 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 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 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: 6075.8487 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -1554.3284 Final Estimated RMS Z Scores: bonds: 0.5948 angles: 1.2727 torsions: N/A planes: 1.8234 non-bonded: 0.0119 chiral vol: 1.0677 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.3620 Refinement elapsed time: 0.0940 ---------------------------------------------- ---------------------------------------------- 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 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 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: 6552.9192 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 67) at -1060.0089 Final Estimated RMS Z Scores: bonds: 0.5084 angles: 1.1886 torsions: N/A planes: 1.8055 non-bonded: 0.0089 chiral vol: 0.9847 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.5680 Refinement elapsed time: 0.2050 ---------------------------------------------- ---------------------------------------------- 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 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 3.3564 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 FAIL close enough with closer than dist_crit 5.9094 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: 6788.8543 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -816.0399 Final Estimated RMS Z Scores: bonds: 0.4547 angles: 1.1272 torsions: N/A planes: 1.7949 non-bonded: 0.0073 chiral vol: 0.9304 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.7660 Refinement elapsed time: 0.1980 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 39 read successfully DEBUG:: there were 0 types with no dictionary ---------------------------------------------- ---------------------------------------------- ERROR:: A: last_restraints no cleared up ---------------------------------------------- ---------------------------------------------- INFO:: created 52 restraints created 23 bond restraints created 25 angle restraints created 0 plane restraints created 4 chiral vol restraints FAIL close enough with closer than dist_crit 3.4424 FAIL close enough with closer than dist_crit 3.4424 FAIL close enough with closer than dist_crit 3.4424 FAIL close enough with closer than dist_crit 3.4424 FAIL close enough with closer than dist_crit 5.0678 FAIL close enough with closer than dist_crit 5.0678 FAIL close enough with closer than dist_crit 5.0678 FAIL close enough with closer than dist_crit 5.0678 FAIL close enough with closer than dist_crit 3.2836 FAIL close enough with closer than dist_crit 3.2836 FAIL close enough with closer than dist_crit 3.2836 FAIL close enough with closer than dist_crit 3.2836 Link restraints: 3 bond links 8 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 3 bond links 9 angle links 6 plane links 3 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 764 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -1126.4717 Initial RMS Z values bonds: 1.6203 angles: 1.0091 torsions: N/A planes: 0.7374 non-bonded: 0.0256 chiral vol: 0.5795 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 12) at -1280.6700 Final Estimated RMS Z Scores: bonds: 0.1538 angles: 0.4838 torsions: N/A planes: 0.3706 non-bonded: 0.0026 chiral vol: 0.2489 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.8320 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:38_2018_modification_0.pdb.gz INFO:: replace_coords: 27 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it results: (#t #t #t #t) PASS: Hs are correctly swapped on a TYR Entered testcase - Splitting residue leaves no atoms with negative occupancy PASS: Splitting residue leaves no atoms with negative occupancy Entered testcase - Pepflip flips the correct alt confed atoms PASS: Pepflip flips the correct alt confed atoms Entered testcase - Correction of CISPEP test PASS: Correction of CISPEP test Entered testcase - H on a N moves on cis-trans convert dd: 3.29414331487717 PASS: H on a N moves on cis-trans convert Entered testcase - HA on a ALA exists after mutation to GLY PASS: HA on a ALA exists after mutation to GLY Entered testcase - Refine Zone with Alt conf refined moved: d=0.105058776170264 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.28877098598258 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 2.018" 2.01755118370056) ("Angles" "Angles: 2.047" 2.04696083068848) ("Planes" "Planes: 1.691" 1.69054794311523) ("Non-bonded" "Non-bonded: 0.257" 0.257192015647888) ("Chirals" "Chirals: 2.099" 2.09890389442444))) ow factor: 1.96349096298218 INFO:: setting refinement weight to 15.5630042791688 refinement results: ("" 0 (("Bonds" "Bonds: 0.785" 0.784663140773773) ("Angles" "Angles: 1.397" 1.39722752571106) ("Planes" "Planes: 1.834" 1.83387017250061) ("Non-bonded" "Non-bonded: 0.137" 0.13665597140789) ("Chirals" "Chirals: 1.244" 1.24419295787811))) ow factor: 1.31498844921589 INFO:: setting refinement weight to 9.00014625281004 refinement results: ("" 0 (("Bonds" "Bonds: 0.595" 0.594846904277802) ("Angles" "Angles: 1.273" 1.27267050743103) ("Planes" "Planes: 1.823" 1.8234121799469) ("Non-bonded" "Non-bonded: 0.109" 0.109081700444221) ("Chirals" "Chirals: 1.068" 1.06765615940094))) ow factor: 1.18964643776417 INFO:: setting refinement weight to 6.35936472246963 refinement results: ("" 0 (("Bonds" "Bonds: 0.508" 0.508431255817413) ("Angles" "Angles: 1.189" 1.18864774703979) ("Planes" "Planes: 1.805" 1.80547392368317) ("Non-bonded" "Non-bonded: 0.095" 0.094509668648243) ("Chirals" "Chirals: 0.985" 0.98465770483017))) ow factor: 1.12180265784264 INFO:: setting refinement weight to 5.05336641370355 refinement results: ("" 0 (("Bonds" "Bonds: 0.455" 0.454684764146805) ("Angles" "Angles: 1.127" 1.12720894813538) ("Planes" "Planes: 1.795" 1.79487359523773) ("Non-bonded" "Non-bonded: 0.085" 0.0853942930698395) ("Chirals" "Chirals: 0.930" 0.93038809299469))) ow factor: 1.07678885012865 PASS: Refinement gives useful results Entered testcase - Neighbour-Refine doesn't destroy disulfide bonds bond-length-within-tolerance? bond-length 2.03007044242803 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.59543800354 27.5053157806396 11.2305965423584)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7643661499023 26.9790077209473 9.45478534698486)) INFO:: created 52 restraints created 23 bond restraints created 25 angle restraints created 0 plane restraints created 4 chiral vol restraints FAIL close enough with closer than dist_crit 3.4428 FAIL close enough with closer than dist_crit 3.4428 FAIL close enough with closer than dist_crit 3.4428 FAIL close enough with closer than dist_crit 3.4428 FAIL close enough with closer than dist_crit 5.1461 FAIL close enough with closer than dist_crit 5.1461 FAIL close enough with closer than dist_crit 5.1461 FAIL close enough with closer than dist_crit 5.1461 FAIL close enough with closer than dist_crit 3.3222 FAIL close enough with closer than dist_crit 3.3222 FAIL close enough with closer than dist_crit 3.3222 FAIL close enough with closer than dist_crit 3.3222 Link restraints: 3 bond links 8 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 3 bond links 9 angle links 6 plane links 3 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 764 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -1280.6700 Initial RMS Z values bonds: 0.1538 angles: 0.4838 torsions: N/A planes: 0.3706 non-bonded: 0.0026 chiral vol: 0.2489 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -1280.6721 Final Estimated RMS Z Scores: bonds: 0.1535 angles: 0.4837 torsions: N/A planes: 0.3720 non-bonded: 0.0026 chiral vol: 0.2497 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.8620 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:38_2018_modification_1.pdb.gz INFO:: replace_coords: 27 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it bond-length-within-tolerance? bond-length 2.03006743488853 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.5953388214111 27.5053443908691 11.2306146621704)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7642688751221 26.9790706634521 9.45479583740234)) 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 40 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_11:44:38_2018_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring 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 41 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Wed_Sep_19_11:44:38_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Wed_Sep_19_11:44:38_2018_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/coords-B3A.pdb PDB file /home/paule/data/greg-data/coords-B3A.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 43 read successfully DEBUG:: there were 1 types with no dictionary INFO:: created 11 restraints created 5 bond restraints created 5 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 5 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2.9511 Initial RMS Z values bonds: 0.6619 angles: 0.3737 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.2500 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 23) at 0.0000 Final Estimated RMS Z Scores: bonds: 0.0014 angles: 0.0027 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0012 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.1000 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Wed_Sep_19_11:44:38_2018_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/lib-B3A.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/lib-B3A.cif had no bond restraints INFO:: created 11 restraints created 5 bond restraints created 5 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 5 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 0.0000 Initial RMS Z values bonds: 0.0014 angles: 0.0027 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0012 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at 0.0000 Final Estimated RMS Z Scores: bonds: 0.0003 angles: 0.0026 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0007 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.2140 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Wed_Sep_19_11:44:38_2018_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Welcome to Coot INFO:: created 11 restraints created 5 bond restraints created 5 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 5 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 3.0185 Initial RMS Z values bonds: 0.6708 angles: 0.3753 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.2536 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 16) at 0.0000 Final Estimated RMS Z Scores: bonds: 0.0004 angles: 0.0004 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0002 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.3290 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Wed_Sep_19_11:44:38_2018_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0290 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0250 seconds for FFT INFO:: 0.0040 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0600 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. 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 45 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_11:44:39_2018_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.0897,14.9163) B-factor: 45.0000 debug:: add_OXT_to_residue() returns istat 1 WARNING:: This residue already has an OXT - aborting debug:: add_OXT_to_residue() returns istat 0 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 46 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_11:44:39_2018_modification_0.pdb.gz 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 47 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_11:44:39_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0404 rms devi: 0.0472 max devi: 0.0833 min devi: 0.0130 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 48 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_11:44:39_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0435 rms devi: 0.0478 max devi: 0.0740 min devi: 0.0148 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 49 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_11:44:39_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0394 rms devi: 0.0445 max devi: 0.0695 min devi: 0.0151 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0260 seconds for FFT INFO:: 0.0040 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0000 seconds for contour map INFO:: 0.0590 seconds in total 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 2.2000 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.0290 seconds to read MTZ file INFO:: 0.0320 seconds to initialize map INFO:: 0.0370 seconds for FFT INFO:: 0.0060 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0518 Map minimum: ..... -0.9217 INFO:: 0.0010 seconds for contour map INFO:: 0.1050 seconds in total 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 52 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.0014 st.d: 0.3055 Map statistics: min: -0.8957, max: 2.7638 -0.8500 7 -0.7585 47 -0.6670 345 -0.5755 1966 -0.4840 7547 -0.3926 21145 -0.3011 36984 -0.2096 49747 -0.1181 62502 -0.0266 78146 0.0649 56227 0.1564 31741 0.2479 15372 0.3393 9396 0.4308 7278 0.5223 6354 0.6138 5287 0.7053 4622 0.7968 3865 0.8883 3168 0.9798 2366 1.0712 1769 1.1627 1258 1.2542 879 1.3457 637 1.4372 417 1.5287 237 1.6202 135 1.7117 69 1.8031 46 1.8946 18 1.9861 8 2.0776 2 2.1691 6 2.2606 2 2.3521 0 2.4436 1 2.5350 3 2.6265 0 2.7180 1 2.8095 0 PASS: Neighbour-Refine doesn't destroy disulfide bonds Entered testcase - Rigid Body Refine Alt Conf Waters PASS: Rigid Body Refine Alt Conf Waters Entered testcase - Setting multiple atom attributes PASS: Setting multiple atom attributes Entered testcase - Tweak Alt Confs on Active Residue PASS: Tweak Alt Confs on Active Residue Entered testcase - Backrub rotamer PASS: Backrub rotamer Entered testcase - Libcif horne PASS: Libcif horne Entered testcase - Refmac Parameters Storage PASS: Refmac Parameters Storage Entered testcase - OXT is added before TER record - add only one found TER "TER 25 ASP A 14 " PASS: OXT is added before TER record - add only one Entered testcase - The position of the oxygen after a mutation PASS: The position of the oxygen after a mutation Entered testcase - TER is at the end of a nucleotide after mutation PASS: TER is at the end of a nucleotide after mutation Entered testcase - C7 is removed on mutation from a DC PASS: C7 is removed on mutation from a DC Entered testcase - C7 is added on mutation to a DC DEBUG:: atoms is (" P " " OP1" " OP2" " O5'" " C5'" " C4'" " O4'" " C3'" " O3'" " C2'" " C1'" " N1 " " C2 " " N3 " " C4 " " C5 " " C6 " " O2 " " O4 " " C7 ") PASS: C7 is added on mutation to a DC Entered testcase - Mask and difference map high-values: (0.966407895088196 0.928917825222015 0.952126145362854 0.646193742752075 0.637681543827057 0.801941633224487 0.734838247299194 1.07139241695404 0.994847536087036 0.931116282939911 0.78803938627243) 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: -0.0014 st.d: 0.0603 Map statistics: min: -2.9772, max: 0.7461 -2.9306 1 -2.8376 1 -2.7445 1 -2.6514 2 -2.5583 2 -2.4652 0 -2.3721 2 -2.2791 1 -2.1860 1 -2.0929 4 -1.9998 2 -1.9067 3 -1.8137 4 -1.7206 4 -1.6275 8 -1.5344 11 -1.4413 15 -1.3482 33 -1.2552 33 -1.1621 49 -1.0690 65 -0.9759 120 -0.8828 145 -0.7898 159 -0.6967 202 -0.6036 249 -0.5105 275 -0.4174 291 -0.3243 411 -0.2313 440 -0.1382 581 -0.0451 300752 0.0480 101991 0.1411 1213 0.2341 1098 0.3272 767 0.4203 463 0.5134 156 0.6065 36 0.6995 8 0.7926 1 diff-high-values: (0.00350911822170019 -6.19744881987572e-4 0.00425338884815574 0.00702545186504722 0.00246794405393302 0.0033501957077533 0.00518705137073994 0.00365039915777743 0.00318349059671164 0.00567070674151182 0.00321404589340091) diff-low-values: (-0.869144320487976 -0.88269180059433 -1.18596041202545 -1.16333603858948 -1.04177522659302 -0.848253965377808 -0.827702522277832 -0.704876363277435 -0.9398592710495 -0.532725632190704) 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 55 read successfully DEBUG:: there were 0 types with no dictionary 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0280 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0610 seconds in total 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 1.8000 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0110 seconds to initialize map INFO:: 0.0280 seconds for FFT INFO:: 0.0040 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0144 Map minimum: ..... -0.8957 INFO:: 0.0010 seconds for contour map INFO:: 0.0720 seconds in total 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 2.5000 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0460 seconds to initialize map INFO:: 0.0490 seconds for FFT INFO:: 0.0090 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0713 Map minimum: ..... -0.8775 INFO:: 0.0020 seconds for contour map INFO:: 0.1340 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 128, 160, 80) by 1.0000 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1.0000 Map statistics: mean: 0.0000 st.d: 0.3111 Map statistics: min: -0.8941, max: 3.0071 -0.8453 8 -0.7478 64 -0.6503 542 -0.5527 3067 -0.4552 12045 -0.3577 29986 -0.2601 46658 -0.1626 61563 -0.0651 73639 0.0324 68489 0.1300 41912 0.2275 19494 0.3250 11050 0.4226 8221 0.5201 7074 0.6176 5839 0.7152 5071 0.8127 4183 0.9102 3295 1.0078 2384 1.1053 1722 1.2028 1175 1.3004 843 1.3979 560 1.4954 325 1.5929 179 1.6905 90 1.7880 59 1.8855 23 1.9831 9 2.0806 8 2.1781 6 2.2757 2 2.3732 2 2.4707 4 2.5683 3 2.6658 2 2.7633 2 2.8608 1 2.9584 0 3.0559 1 Map statistics: mean: -0.0000 st.d: 0.0011 Map statistics: min: -0.0109, max: 0.0109 -0.0107 1 -0.0101 1 -0.0096 0 -0.0090 1 -0.0085 3 -0.0079 2 -0.0074 4 -0.0068 7 -0.0063 25 -0.0058 37 -0.0052 103 -0.0047 260 -0.0041 640 -0.0036 1269 -0.0030 2611 -0.0025 5434 -0.0019 10529 -0.0014 21799 -0.0008 51978 -0.0003 109495 0.0003 110465 0.0008 52013 0.0013 20447 0.0019 9606 0.0024 5236 0.0030 2974 0.0035 1857 0.0041 1167 0.0046 683 0.0052 388 0.0057 223 0.0063 139 0.0068 86 0.0074 56 0.0079 25 0.0084 16 0.0090 7 0.0095 4 0.0101 4 0.0106 4 0.0112 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 61 read successfully DEBUG:: there were 2 types with no dictionary 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: 2651.7158 Initial RMS Z values bonds: 6.1616 angles: 2.8528 torsions: N/A planes: 0.0835 non-bonded: 0.2115 chiral vol: 0.9035 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 887) at 15.9904 Final Estimated RMS Z Scores: bonds: 0.1009 angles: 0.4225 torsions: N/A planes: 0.0264 non-bonded: 0.0002 chiral vol: 0.1561 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.8990 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-3.pdb_Wed_Sep_19_11:44:40_2018_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it PASS: Mask and difference map Entered testcase - Skeletonize a map PASS: Skeletonize a map Entered testcase - Simple Averaged maps INFO:: map sigmas: normal 0.311081498861313 and diff-map: 0.0010762547608465 PASS: Simple Averaged maps Entered testcase - Make a glycosidic linkage bond-length: 2.2472998823295: bond-length: 1.44437928674295: bond-length-within-tolerance? bond-length 1.44437928674295 with target 1.439 and tolerance 0.04 for atom ((" O4 " "") (1.0 20.0 " O" "") (-3.95734977722168 20.753511428833 1.51749432086945)) is ((" C1 " "") (1.0 20.0 " C" "") (-3.19250345230103 21.6129570007324 2.39076113700867)) 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 62 read successfully DEBUG:: there were 1 types with no dictionary 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:: 0.0290 seconds to read MTZ file INFO:: 0.0100 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0000 seconds for contour map INFO:: 0.0610 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_11:44:40_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:44:40_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_11:44:40_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 697 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 66106.8754 Initial RMS Z values bonds: 0.3607 angles: 0.6064 torsions: N/A planes: 0.6834 non-bonded: 95.2223 chiral vol: 0.4449 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -135.3526 Final Estimated RMS Z Scores: bonds: 1.9226 angles: 1.1808 torsions: N/A planes: 0.9305 non-bonded: 0.0607 chiral vol: 0.1794 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.6970 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:44:40_2018_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. (process:423): 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 649 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 20487.3699 Initial RMS Z values bonds: 1.9226 angles: 1.1808 torsions: N/A planes: 0.9305 non-bonded: 31.8413 chiral vol: 0.1794 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -126.9103 Final Estimated RMS Z Scores: bonds: 1.8223 angles: 1.2328 torsions: N/A planes: 0.9307 non-bonded: 0.0644 chiral vol: 0.4805 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.8350 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Sep_19_11:44:40_2018_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it PASS: Make a glycosidic linkage Entered testcase - Refine an NAG-ASN Link bond-length-within-tolerance? bond-length 1.57435909387613 with target 1.43 and tolerance 0.2 for atom ((" ND2" "") (1.0 16.9300003051758 " N" "") (-14.1817655563354 0.163284555077553 -7.75624132156372)) is ((" C1 " "") (1.0 45.0 " C" "") (-12.7525463104248 -0.106723859906197 -7.15371799468994)) 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 64 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: 4.9970 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.4516 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.2482 Final Estimated RMS Z Scores: bonds: 0.0122 angles: 0.0949 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.1454 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.9280 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:44:41_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: undo molecule number set to: 64 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:44:41_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_11:44:41_2018_modification_0.pdb.gz PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:44:41_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:: 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: 4.9970 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.4516 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.2482 Final Estimated RMS Z Scores: bonds: 0.0122 angles: 0.0949 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.1454 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.0020 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Wed_Sep_19_11:44:41_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it PASS: Refine an NAG-ASN Link Entered testcase - Test for flying hydrogens on undo bond-length-within-tolerance? bond-length 0.960061691781605 with target 0.96 and tolerance 0.02 for atom (("HG11" "") (1.0 20.0 " H" "") (3.4704897403717 -0.190908700227737 -1.96913886070251)) is ((" CG1" "") (1.0 20.0 " C" "") (2.87013721466064 -0.207151547074318 -1.22011852264404)) 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 65 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: 903.0633 Initial RMS Z values bonds: 5.6211 angles: 3.4330 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.7534 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 165) at 0.4747 Final Estimated RMS Z Scores: bonds: 0.0094 angles: 0.1210 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.1385 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.0760 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_11:44:41_2018_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it PASS: Test for flying hydrogens on undo Entered testcase - Test for regularization and mangling of hydrogen names from a PDB v 3.0 bond-length-within-tolerance? bond-length 0.959993508181978 with target 0.96 and tolerance 0.02 for atom (("HD11" "") (1.0 10.5299997329712 " H" "") (-10.1156616210938 6.52059507369995 7.01407289505005)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977)) bond-length-within-tolerance? bond-length 0.96002780270247 with target 0.96 and tolerance 0.02 for atom (("HD12" "") (1.0 10.1300001144409 " H" "") (-9.7598762512207 5.68341684341431 5.73144054412842)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977)) bond-length-within-tolerance? bond-length 0.959946651623676 with target 0.96 and tolerance 0.02 for atom (("HD13" "") (1.0 10.5600004196167 " H" "") (-11.027907371521 5.31390428543091 6.58492517471313)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977)) bond-length-within-tolerance? bond-length 0.959995371308682 with target 0.96 and tolerance 0.02 for atom (("HD21" "") (1.0 10.1499996185303 " H" "") (-7.9939432144165 3.15288591384888 7.14437961578369)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627)) bond-length-within-tolerance? bond-length 0.960016201142166 with target 0.96 and tolerance 0.02 for atom (("HD22" "") (1.0 10.3000001907349 " H" "") (-9.20783233642578 3.14652538299561 6.14453363418579)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627)) bond-length-within-tolerance? bond-length 0.959897847605806 with target 0.96 and tolerance 0.02 for atom (("HD23" "") (1.0 10.6499996185303 " H" "") (-8.02846336364746 4.16698122024536 5.94336414337158)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627)) 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: 2864.9130 Initial RMS Z values bonds: 1.1515 angles: 0.8476 torsions: N/A planes: 3.0558 non-bonded: 79.8585 chiral vol: 0.7578 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 88) at -329.7893 Final Estimated RMS Z Scores: bonds: 0.2710 angles: 0.2153 torsions: N/A planes: 0.2251 non-bonded: 0.0089 chiral vol: 0.0782 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.1380 Refinement elapsed time: 0.0130 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:41_2018_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it PASS: Test for regularization and mangling of hydrogen names from a PDB v 3.0 Entered testcase - correct matching dictionary names from test name PASS: correct matching dictionary names from test name Entered testcase - update monomer restraints Bond-length: 2.62808176200628: bond-length-within-tolerance? bond-length 2.62808176200628 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.3068313598633 4.49463319778442 19.7860126495361)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.548095703125 6.70595741271973 19.0959968566895)) 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: 2243.4873 Initial RMS Z values bonds: 14.6471 angles: 0.2153 torsions: N/A planes: 0.2251 non-bonded: 0.0000 chiral vol: 0.0782 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 122) at -363.4672 Final Estimated RMS Z Scores: bonds: 0.0903 angles: 0.1119 torsions: N/A planes: 0.2937 non-bonded: 0.0000 chiral vol: 0.0207 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.1680 Refinement elapsed time: 0.0130 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:41_2018_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.51450376873725: bond-length-within-tolerance? bond-length 1.51450376873725 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5381164550781 4.9324107170105 19.390796661377)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.2945861816406 6.21128845214844 19.0976295471191)) INFO:: wrote mmCIF "coot-test-ala.cif" 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 67 read successfully DEBUG:: there were 1 types with no dictionary Welcome to Coot WARNING:: bond_restraint_length 4 should be 5 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: 4835.2347 Initial RMS Z values bonds: 0.0120 angles: 0.0065 torsions: N/A planes: 0.0000 non-bonded: 689.9273 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 78) at -105.9625 Final Estimated RMS Z Scores: bonds: 0.0639 angles: 0.0542 torsions: N/A planes: 0.0557 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.3890 Refinement elapsed time: 0.0210 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Wed_Sep_19_11:44:42_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 68 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_11:44:42_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_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_11:44:42_2018_modification_2.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_2018_modification_3.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_2018_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_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_11:44:42_2018_modification_6.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_2018_modification_7.pdb.gz 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_11:44:42_2018_modification_0.pdb.gz FAIL close enough with closer than dist_crit 25.3707 FAIL close enough with closer than dist_crit 25.3707 FAIL close enough with closer than dist_crit 25.3707 FAIL close enough with closer than dist_crit 25.3707 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_2018_modification_1.pdb.gz 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:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:42_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_2018_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. 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 72 read successfully DEBUG:: there were 0 types with no dictionary in new_molecule_by_residue_type_selection Something bad happened - No residues selected in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:42_2018_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint 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 73 read successfully DEBUG:: there were 0 types with no dictionary INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.0000%] 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 74 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 74 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -3.0000 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 150.0000 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_11:44:42_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: 200721544 "A" 1 ""] -> ASP [spec: 200721544 "A" 2 ""] -> VAL [spec: 200721544 "A" 3 ""] -> SER [spec: 200721544 "A" 11 ""] -> LEU [spec: 200721544 "A" 12 ""] -> PRO [spec: 200721544 "A" 13 ""] -> PRO [spec: 120768360 "A" 62 ""] -> PRO [spec: 120768360 "A" 63 ""] -> GLY Deletions: [spec: 120768360 "A" 25 ""] [spec: 120768360 "A" 34 ""] Mutations: [spec: 120768360 "A" 24 ""] -> SER [spec: 120768360 "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:: 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 75 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_11:44:42_2018_modification_0.pdb.gz 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 76 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_11:44:42_2018_modification_0.pdb.gz 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 77 read successfully DEBUG:: there were 1 types with no dictionary 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 1.5000 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.0220 seconds to read MTZ file INFO:: 0.0060 seconds to initialize map INFO:: 0.0130 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.2604 Map maximum: ..... 1.7179 Map minimum: ..... -1.0339 INFO:: 0.0000 seconds for contour map INFO:: 0.0440 seconds in total INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Wed_Sep_19_11:44:43_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.8340 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Wed_Sep_19_11:44:43_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0000 rms devi: 0.0000 max devi: 0.0000 min devi: 0.0000 INFO:: 5 matched atoms had: mean devi: 0.0121 rms devi: 0.0134 max devi: 0.0214 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0846 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1123 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0847 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0133 max devi: 0.0213 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.0002 rms devi: 0.0002 max devi: 0.0003 min devi: 0.0002 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0846 INFO:: 5 matched atoms had: mean devi: 0.2673 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1124 INFO:: 5 matched atoms had: mean devi: 0.0001 rms devi: 0.0001 max devi: 0.0001 min devi: 0.0001 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0134 max devi: 0.0214 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.0001 rms devi: 0.0001 max devi: 0.0001 min devi: 0.0001 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0134 max devi: 0.0213 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.2703 rms devi: 0.3351 max devi: 0.5361 min devi: 0.0848 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_11:44:43_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Sep_19_11:44:43_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2690 rms devi: 0.3372 max devi: 0.5475 min devi: 0.0818 INFO:: 5 matched atoms had: mean devi: 0.0000 rms devi: 0.0000 max devi: 0.0000 min devi: 0.0000 INFO:: 5 matched atoms had: mean devi: 0.0121 rms devi: 0.0134 max devi: 0.0214 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0846 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1123 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0847 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0133 max devi: 0.0213 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.0002 rms devi: 0.0002 max devi: 0.0003 min devi: 0.0002 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0846 INFO:: 5 matched atoms had: mean devi: 0.2673 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1124 INFO:: 5 matched atoms had: mean devi: 0.0001 rms devi: 0.0001 max devi: 0.0001 min devi: 0.0001 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0134 max devi: 0.0214 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.0001 rms devi: 0.0001 max devi: 0.0001 min devi: 0.0001 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0134 max devi: 0.0213 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.2703 rms devi: 0.3351 max devi: 0.5361 min devi: 0.0848 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_11:44:43_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Sep_19_11:44:43_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2690 rms devi: 0.3372 max devi: 0.5475 min devi: 0.0818 INFO:: 5 matched atoms had: mean devi: 0.0059 rms devi: 0.0067 max devi: 0.0101 min devi: 0.0026 INFO:: 5 matched atoms had: mean devi: 0.0073 rms devi: 0.0078 max devi: 0.0126 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.0878 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5339 min devi: 0.0879 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.0072 rms devi: 0.0077 max devi: 0.0124 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.0057 rms devi: 0.0066 max devi: 0.0100 min devi: 0.0024 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.0878 INFO:: 5 matched atoms had: mean devi: 0.2677 rms devi: 0.3265 max devi: 0.5055 min devi: 0.1047 INFO:: 5 matched atoms had: mean devi: 0.0059 rms devi: 0.0067 max devi: 0.0101 min devi: 0.0025 INFO:: 5 matched atoms had: mean devi: 0.0072 rms devi: 0.0078 max devi: 0.0125 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.0058 rms devi: 0.0066 max devi: 0.0100 min devi: 0.0025 INFO:: 5 matched atoms had: mean devi: 0.0072 rms devi: 0.0077 max devi: 0.0124 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3266 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3365 max devi: 0.5339 min devi: 0.0880 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_11:44:43_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.0923 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043 rms devi: 0.0048 max devi: 0.0074 min devi: 0.0019 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.3260 max devi: 0.5019 min devi: 0.0927 INFO:: 5 matched atoms had: mean devi: 0.0059 rms devi: 0.0067 max devi: 0.0101 min devi: 0.0026 INFO:: 5 matched atoms had: mean devi: 0.0073 rms devi: 0.0078 max devi: 0.0126 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.0878 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5339 min devi: 0.0879 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.0072 rms devi: 0.0077 max devi: 0.0124 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.0057 rms devi: 0.0066 max devi: 0.0100 min devi: 0.0024 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.0878 INFO:: 5 matched atoms had: mean devi: 0.2677 rms devi: 0.3265 max devi: 0.5055 min devi: 0.1047 INFO:: 5 matched atoms had: mean devi: 0.0059 rms devi: 0.0067 max devi: 0.0101 min devi: 0.0025 INFO:: 5 matched atoms had: mean devi: 0.0072 rms devi: 0.0078 max devi: 0.0125 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.0058 rms devi: 0.0066 max devi: 0.0100 min devi: 0.0025 INFO:: 5 matched atoms had: mean devi: 0.0072 rms devi: 0.0077 max devi: 0.0124 min devi: 0.0046 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3266 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3365 max devi: 0.5339 min devi: 0.0880 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_11:44:43_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.0923 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043 rms devi: 0.0048 max devi: 0.0074 min devi: 0.0019 INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Sep_19_11:44:43_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.3260 max devi: 0.5019 min devi: 0.0927 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_11:44:43_2018_modification_0.pdb.gz 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 84 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_some-waters-with-ter.pdb_Wed_Sep_19_11:44:43_2018_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3.0000,4.0000,5.0000) B-factor: 45.0000 added to molecule 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 85 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 2.0000 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3115 INFO:: Using density cut-off: 0.6230 (2.0000 sigma) (mean -0.0338 stdev: 0.1463) INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4000 3.2000 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 59.89, 3.041, -4.33) is too big to be water INFO:: cluster at xyz = ( 70.01, 19.08, 18.6) is too big to be water INFO:: cluster at xyz = ( 52.98, 9.035, 20.15) is too big to be water INFO:: found 54 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_11:44:43_2018_modification_0.pdb.gz INFO:: Adding to solvent chain: D 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:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:43_2018_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 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 87 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_11:44:46_2018_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules 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 88 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_11:44:46_2018_modification_0.pdb.gz INFO:: moved 181 water molecules 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:: 0.0290 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0030 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:: 0.0530 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_11:44:46_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:46_2018_modification_1.pdb.gz 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" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 91 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 91 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: (44.8780,12.9550,8.7610) 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) 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_11:44:46_2018_modification_0.pdb.gz 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 92 read successfully DEBUG:: there were 0 types with no dictionary 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 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 93 read successfully DEBUG:: there were 1 types with no dictionary 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 94 read successfully DEBUG:: there were 0 types with no dictionary 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 95 read successfully DEBUG:: there were 1 types with no dictionary -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0.0000 0.0000 0.3333 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: (62.5724,-20.4973,95.4680) B-factor: 45.2600 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (64.4244,-37.8536,121.3880) 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) | 0.8045, 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: (62.5724,-20.4973,95.4680) B-factor: 45.2600 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (-18.2586,-63.0428,111.4250) 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) | -0.5596, -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: (62.5724,-20.4973,95.4680) B-factor: 45.2600 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (-0.2911,-72.4822,94.4690) 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) | -0.4782, -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:: 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_11:44:46_2018_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:46_2018_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Sep_19_11:44:46_2018_modification_1.pdb.gz INFO:: Matching/moving molecule number 100 to 99 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.0353 rms devi: 0.0378 max devi: 0.0545 min devi: 0.0167 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_11:44:46_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) PASS: update monomer restraints Entered testcase - Write mmCIF restraints correctly PASS: Write mmCIF restraints correctly Entered testcase - Refinement OK with zero bond esd PASS: Refinement OK with zero bond esd Entered testcase - Change Chain IDs and Chain Sorting PASS: Change Chain IDs and Chain Sorting Entered testcase - Chain-ids in links change also on change chain id PASS: Chain-ids in links change also on change chain id Entered testcase - Replace Fragment distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) PASS: Replace Fragment Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () PASS: Residues in Region of Residue Entered testcase - Residues in region of a point PASS: Residues in region of a point Entered testcase - Empty molecule on type selection PASS: Empty molecule on type selection Entered testcase - Set Rotamer PASS: Set Rotamer Entered testcase - Rotamer names and scores are correct Rotamer 0 : "m-85" 100.0 Rotamer 1 : "t80" 90.1668395996094 Rotamer 2 : "p90" 50.7077865600586 Rotamer 3 : "m -30 " 21.4231548309326 Rotamer 4 : "m -30 " 21.4231548309326 PASS: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions ::::: (74 "A" 1 "") #f #f ::::: (74 "A" 4 "") #t #t ::::: (74 "A" 57 "") #t #t ::::: (74 "A" 60 "") #f #f ::::: (74 "A" 61 "") #f #f ::::: (74 "A" 92 "") #t #t ::::: (74 "A" 94 "") #f #f results: (#t #t #t #t #t #t #t) PASS: Align and mutate a model with deletions Entered testcase - renumbered residues should be in seqnum order PASS: renumbered residues should be in seqnum order Entered testcase - Autofit Rotamer on Residues with Insertion codes PASS: Autofit Rotamer on Residues with Insertion codes Entered testcase - RNA base has correct residue type after mutation mutated base to type "C" - was "A" mutated base to type "Cr" - was "A" PASS: RNA base has correct residue type after mutation Entered testcase - resname from serial number doesnt crash on silly input PASS: resname from serial number doesnt crash on silly input Entered testcase - DNA bases are the correct residue type after mutation mutated base to type "DC" mutated base to type "DG" mutated base to type "DA" mutated base to type "DT" mutated base to type "Cd" mutated base to type "Gd" mutated base to type "Ad" mutated base to type "Td" PASS: DNA bases are the correct residue type after mutation Entered testcase - SegIDs are correct after mutate PASS: SegIDs are correct after mutate Entered testcase - TER on water chain is removed on adding a water by hand PASS: TER on water chain is removed on adding a water by hand Entered testcase - TER on water chain is removed on adding waters automatically PASS: TER on water chain is removed on adding waters automatically Entered testcase - Adding atoms to Many-Chained Molecule PASS: Adding atoms to Many-Chained Molecule Entered testcase - Arrange waters round protein PASS: Arrange waters round protein Entered testcase - Correct Segid After Add Terminal Residue PASS: Correct Segid After Add Terminal Residue Entered testcase - Correct Segid after NCS residue range copy PASS: Correct Segid after NCS residue range copy Entered testcase - Merge Water Chains PASS: Merge Water Chains Entered testcase - Consolidated merge -------- starting chain list ----------- DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "") DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K") PASS: Consolidated merge Entered testcase - Test for good chain ids after a merge chain-ids: ("AAA" "B" "B-chain") --- chain-ids: ("AAA" "B" "B-chain" "AAA_2") PASS: Test for good chain ids after a merge Entered testcase - LSQ by atom bond-length-within-tolerance? bond-length 0.110921496735531 with target 0.0 and tolerance 0.2 for atom ((" C " "") (1.0 15.5799999237061 " C" "") (56.8940010070801 1.29299998283386 19.6700000762939)) is ((" C " "") (1.0 16.7800006866455 " C" "") (56.8856086730957 1.18242847919464 19.6726627349854)) 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:: 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 102 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 101 to 102 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.5023 rms devi: 0.5938 max devi: 1.6785 min devi: 0.0432 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_11:44:47_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 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_11:44:47_2018_modification_0.pdb.gz 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 104 read successfully DEBUG:: there were 0 types with no dictionary 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 105 read successfully DEBUG:: there were 7 types with no dictionary 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 106 read successfully DEBUG:: there were 0 types with no dictionary 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:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 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:: 0.0000 seconds for contour map INFO:: 0.0510 seconds in total masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:44:47_2018_modification_0.pdb.gz INFO:: replace_coords: 745 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.9028 13.6977 9.2374 90.0000 98.2110 90.0000 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 108 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.3243 34.3243 11.0887 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 41 2 2" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 109 read successfully INFO:: spacegroup: I 41 2 2 LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 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 110 read successfully Map statistics: mean: -0.0001 st.d: 0.3052 Map statistics: min: -0.7810, max: 6.0791 -0.6953 231 -0.5238 4724 -0.3523 24910 -0.1808 55291 -0.0093 95241 0.1622 40930 0.3337 7480 0.5052 3968 0.6767 2790 0.8482 2117 1.0197 1738 1.1912 1221 1.3628 888 1.5343 595 1.7058 355 1.8773 240 2.0488 137 2.2203 97 2.3918 62 2.5633 46 2.7348 17 2.9063 17 3.0778 13 3.2493 10 3.4208 7 3.5923 1 3.7638 3 3.9353 7 4.1068 2 4.2783 5 4.4498 1 4.6213 2 4.7928 2 4.9643 0 5.1358 1 5.3073 0 5.4788 0 5.6503 0 5.8218 0 5.9933 1 6.1648 0 Map statistics: mean: -0.0000 st.d: 0.0468 Map statistics: min: -0.2115, max: 0.6486 -0.2008 7 -0.1793 48 -0.1578 209 -0.1363 787 -0.1148 2257 -0.0933 5676 -0.0717 12730 -0.0502 24380 -0.0287 38190 -0.0072 46230 0.0143 43880 0.0358 32484 0.0573 19420 0.0788 9718 0.1003 4120 0.1218 1677 0.1433 718 0.1648 329 0.1863 133 0.2078 77 0.2293 29 0.2508 11 0.2723 13 0.2938 8 0.3153 2 0.3368 2 0.3583 2 0.3798 1 0.4013 1 0.4228 2 0.4443 2 0.4658 1 0.4873 1 0.5088 1 0.5304 1 0.5519 1 0.5734 0 0.5949 0 0.6164 0 0.6379 2 0.6594 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 WARNING:: invalid molecule (204050) for write_shelx_ins_file 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. PASS: LSQ by atom Entered testcase - LSQing changes the space-group and cell to that of the reference molecule PASS: LSQing changes the space-group and cell to that of the reference molecule Entered testcase - set-residue-name sets the correct residue PASS: set-residue-name sets the correct residue Entered testcase - fit-protein-make-specs makes all specs specs: 189 ((104 "A" 1 "") (104 "A" 2 "") (104 "A" 3 "") (104 "A" 4 "") (104 "A" 5 "") (104 "A" 6 "") (104 "A" 7 "") (104 "A" 8 "") (104 "A" 9 "") (104 "A" 10 "") (104 "A" 11 "") (104 "A" 12 "") (104 "A" 13 "") (104 "A" 14 "") (104 "A" 15 "") (104 "A" 16 "") (104 "A" 17 "") (104 "A" 18 "") (104 "A" 19 "") (104 "A" 20 "") (104 "A" 21 "") (104 "A" 22 "") (104 "A" 23 "") (104 "A" 24 "") (104 "A" 25 "") (104 "A" 26 "") (104 "A" 27 "") (104 "A" 28 "") (104 "A" 29 "") (104 "A" 30 "") (104 "A" 31 "") (104 "A" 32 "") (104 "A" 33 "") (104 "A" 34 "") (104 "A" 35 "") (104 "A" 36 "") (104 "A" 37 "") (104 "A" 38 "") (104 "A" 39 "") (104 "A" 40 "") (104 "A" 41 "") (104 "A" 42 "") (104 "A" 43 "") (104 "A" 44 "") (104 "A" 45 "") (104 "A" 46 "") (104 "A" 47 "") (104 "A" 48 "") (104 "A" 49 "") (104 "A" 50 "") (104 "A" 51 "") (104 "A" 52 "") (104 "A" 53 "") (104 "A" 54 "") (104 "A" 55 "") (104 "A" 56 "") (104 "A" 57 "") (104 "A" 58 "") (104 "A" 59 "") (104 "A" 60 "") (104 "A" 61 "") (104 "A" 62 "") (104 "A" 63 "") (104 "A" 64 "") (104 "A" 65 "") (104 "A" 66 "") (104 "A" 67 "") (104 "A" 68 "") (104 "A" 69 "") (104 "A" 70 "") (104 "A" 71 "") (104 "A" 72 "") (104 "A" 73 "") (104 "A" 74 "") (104 "A" 75 "") (104 "A" 76 "") (104 "A" 77 "") (104 "A" 78 "") (104 "A" 79 "") (104 "A" 80 "") (104 "A" 81 "") (104 "A" 82 "") (104 "A" 83 "") (104 "A" 84 "") (104 "A" 85 "") (104 "A" 86 "") (104 "A" 87 "") (104 "A" 88 "") (104 "A" 89 "") (104 "A" 90 "") (104 "A" 91 "") (104 "A" 92 "") (104 "A" 93 "") (104 "B" 1 "") (104 "B" 2 "") (104 "B" 3 "") (104 "B" 4 "") (104 "B" 5 "") (104 "B" 6 "") (104 "B" 7 "") (104 "B" 8 "") (104 "B" 9 "") (104 "B" 10 "") (104 "B" 11 "") (104 "B" 12 "") (104 "B" 13 "") (104 "B" 14 "") (104 "B" 15 "") (104 "B" 16 "") (104 "B" 17 "") (104 "B" 18 "") (104 "B" 19 "") (104 "B" 20 "") (104 "B" 21 "") (104 "B" 22 "") (104 "B" 23 "") (104 "B" 24 "") (104 "B" 25 "") (104 "B" 26 "") (104 "B" 27 "") (104 "B" 28 "") (104 "B" 29 "") (104 "B" 30 "") (104 "B" 31 "") (104 "B" 32 "") (104 "B" 33 "") (104 "B" 34 "") (104 "B" 35 "") (104 "B" 36 "") (104 "B" 37 "") (104 "B" 38 "") (104 "B" 39 "") (104 "B" 40 "") (104 "B" 41 "") (104 "B" 42 "") (104 "B" 43 "") (104 "B" 44 "") (104 "B" 45 "") (104 "B" 46 "") (104 "B" 47 "") (104 "B" 48 "") (104 "B" 49 "") (104 "B" 50 "") (104 "B" 51 "") (104 "B" 52 "") (104 "B" 53 "") (104 "B" 54 "") (104 "B" 55 "") (104 "B" 56 "") (104 "B" 57 "") (104 "B" 58 "") (104 "B" 59 "") (104 "B" 60 "") (104 "B" 61 "") (104 "B" 62 "") (104 "B" 63 "") (104 "B" 64 "") (104 "B" 65 "") (104 "B" 66 "") (104 "B" 67 "") (104 "B" 68 "") (104 "B" 69 "") (104 "B" 70 "") (104 "B" 71 "") (104 "B" 72 "") (104 "B" 73 "") (104 "B" 74 "") (104 "B" 75 "") (104 "B" 76 "") (104 "B" 77 "") (104 "B" 78 "") (104 "B" 79 "") (104 "B" 80 "") (104 "B" 81 "") (104 "B" 82 "") (104 "B" 83 "") (104 "B" 84 "") (104 "B" 85 "") (104 "B" 86 "") (104 "B" 87 "") (104 "B" 88 "") (104 "B" 89 "") (104 "B" 90 "") (104 "B" 91 "") (104 "B" 92 "") (104 "B" 93 "") (104 "B" 94 "") (104 "B" 95 "") (104 "B" 96 "")) PASS: fit-protein-make-specs makes all specs Entered testcase - Phosphate distance in pucker analysis is sane PASS: Phosphate distance in pucker analysis is sane Entered testcase - Fix for Oliver Clarke fit by atom selection bug bl: 0.0363726829001203 PASS: Fix for Oliver Clarke fit by atom selection bug Ended 01-pdb+mtz.scm Running 02-shelx.scm ... Entered testcase - Read small molecule .res file PASS: Read small molecule .res file Entered testcase - Read hollander small molecule .res file PASS: Read hollander small molecule .res file Entered testcase - read shelx insulin with fcf PASS: read shelx insulin with fcf Entered testcase - Write an INS from PDB test PASS: Write an INS from PDB test Entered testcafitting 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_11:44:48_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_11:44:48_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:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Wed_Sep_19_11:44:48_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: (3.0000,-1.0000,60.0000) B-factor: 45.0000 added to molecule INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6000 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3052 INFO:: Using density cut-off: 0.1831 (0.6000 sigma) (mean -0.0203 stdev: 0.1119) INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4000 3.2000 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_11:44:48_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 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 42.1400 83.0300 89.7900 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "P 21 21 21" INFO:: read_file() chain with chain id has 5 residues Symmetry available for this molecule Molecule 115 read successfully LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.0800 32.7600 18.6600 90.0000 101.7300 90.0000 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id has 23 residues Symmetry available for this molecule Molecule 116 read successfully 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. LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL debug:: ## new chain wiith chain-id A INFO:: CELL set to 14.0800 32.7600 18.6600 90.0000 101.7300 90.0000 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id A has 23 residues Symmetry available for this molecule Molecule 117 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.9990 108.9990 107.5550 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 4 2 2" INFO:: read_file() chain with chain id has 4 residues Symmetry available for this molecule Molecule 118 read successfully WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/3GP_from_dict_Wed_Sep_19_11:44:49_2018_modification_0.pdb.gz INFO:: backup file coot-backup/3GP_from_dict_Wed_Sep_19_11:44:49_2018_modification_1.pdb.gz 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 120 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Wed_Sep_19_11:44:49_2018_modification_0.pdb.gz INFO:: comp-id: LIG is marked for non-autoloading - stopping now 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 121 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 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 122 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now 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 123 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Wed_Sep_19_11:44:49_2018_modification_0.pdb.gz ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring 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 124 read successfully DEBUG:: there were 0 types with no dictionary 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 130 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 1.5000 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.1440 seconds to read MTZ file INFO:: 0.0930 seconds to initialize map INFO:: 0.0800 seconds for FFT INFO:: 0.0110 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.1712 Map maximum: ..... 1.3430 Map minimum: ..... -0.6954 INFO:: 0.0000 seconds for contour map INFO:: 0.3280 seconds in total 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 1.5000 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.0880 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0760 seconds for FFT INFO:: 0.0110 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.0334 Map maximum: ..... 0.3661 Map minimum: ..... -0.1917 INFO:: 0.0010 seconds for contour map INFO:: 0.1770 seconds in total INFO:: ligand number 0 is molecule number 124 with wiggly flag: 0 in execute_ligand_search_internal() import maps from mol 131 INFO:: Protein centre at: xyz = ( 58.29, 34.65, 30.63) Map statistics: mean: -0.0217 st.d: 0.0886 Map statistics: min: -0.6954, max: 0.7542 -0.6773 6 -0.6411 8 -0.6048 27 -0.5686 116 -0.5324 354 -0.4961 977 -0.4599 1943 -0.4236 3356 -0.3874 5156 -0.3511 6576 -0.3149 7850 -0.2787 8875 -0.2424 9742 -0.2062 11742 -0.1699 16950 -0.1337 29805 -0.0975 58214 -0.0612 102889 -0.0250 142998 0.0113 471776 0.0475 106846 0.0837 56087 0.1200 21597 0.1562 6911 0.1925 2135 0.2287 920 0.2650 467 0.3012 346 0.3374 216 0.3737 118 0.4099 117 0.4462 80 0.4824 50 0.5186 28 0.5549 33 0.5911 15 0.6274 14 0.6636 11 0.6998 2 0.7361 7 0.7723 0 INFO:: find_clusters map_rms is 0.1711 INFO:: Using density cut-off: 0.1711 (1.0000 sigma) (mean -0.0217 stdev: 0.0886) INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4000 3.2000 INFO:: Finding clusters...done debug:: n_ligands_for_cluster() top_score 4.0420 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: -52.3509 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 21) at -138.1825 Final Estimated RMS Z Scores: bonds: 0.1077 angles: 0.0359 torsions: N/A planes: 0.0530 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 20.3180 Refinement elapsed time: 0.0240 INFO:: backup file coot-backup/Fitted_ligand_#0-0_Wed_Sep_19_11:44:53_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.0180 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: 16.3745 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 115) at -74.4990 Final Estimated RMS Z Scores: bonds: 0.0457 angles: 0.0475 torsions: N/A planes: 0.0448 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 21.2460 Refinement elapsed time: 0.0630 INFO:: backup file coot-backup/Fitted_ligand_#1-0_Wed_Sep_19_11:44:53_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.0901 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: 12.1046 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 111) at -67.1882 Final Estimated RMS Z Scores: bonds: 0.0594 angles: 0.0269 torsions: N/A planes: 0.0249 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 21.7010 Refinement elapsed time: 0.0110 INFO:: backup file coot-backup/Fitted_ligand_#2-0_Wed_Sep_19_11:44:54_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.8588 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: 33.9398 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 28) at -51.2169 Final Estimated RMS Z Scores: bonds: 0.0587 angles: 0.0312 torsions: N/A planes: 0.0505 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 22.3830 Refinement elapsed time: 0.0310 INFO:: backup file coot-backup/Fitted_ligand_#3-0_Wed_Sep_19_11:44:55_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.3913 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: 51.5163 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 103) at -60.2830 Final Estimated RMS Z Scores: bonds: 0.0823 angles: 0.0332 torsions: N/A planes: 0.0947 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 23.4950 Refinement elapsed time: 0.0420 INFO:: backup file coot-backup/Fitted_ligand_#4-0_Wed_Sep_19_11:44:56_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.6844 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: -1.3973 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 111) at -118.9507 Final Estimated RMS Z Scores: bonds: 0.0939 angles: 0.0942 torsions: N/A planes: 0.1517 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 24.3860 Refinement elapsed time: 0.0340 INFO:: backup file coot-backup/Fitted_ligand_#5-0_Wed_Sep_19_11:44:57_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.0961 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: 9.9731 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 123) at -75.3788 Final Estimated RMS Z Scores: bonds: 0.0479 angles: 0.0396 torsions: N/A planes: 0.0942 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 25.2580 Refinement elapsed time: 0.0170 INFO:: backup file coot-backup/Fitted_ligand_#6-0_Wed_Sep_19_11:44:57_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.6363 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: 29.1996 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 58) at -165.0231 Final Estimated RMS Z Scores: bonds: 0.0891 angles: 0.1061 torsions: N/A planes: 0.0787 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 26.2170 Refinement elapsed time: 0.0940 INFO:: backup file coot-backup/Fitted_ligand_#7-0_Wed_Sep_19_11:44:58_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 2.0701 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: 12.6839 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 67) at -93.3095 Final Estimated RMS Z Scores: bonds: 0.1349 angles: 0.1413 torsions: N/A planes: 0.0648 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 26.6200 Refinement elapsed time: 0.0610 INFO:: backup file coot-backup/Fitted_ligand_#8-0_Wed_Sep_19_11:44:59_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: n_ligands_for_cluster() top_score 1.8574 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: 20.8102 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 108) at -66.2402 Final Estimated RMS Z Scores: bonds: 0.0330 angles: 0.0115 torsions: N/A planes: 0.0713 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 27.1830 Refinement elapsed time: 0.0170 INFO:: backup file coot-backup/Fitted_ligand_#9-0_Wed_Sep_19_11:44:59_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:423): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 144 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Wed_Sep_19_11:44:59_2018_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Wed_Sep_19_11:44:59_2018_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Wed_Sep_19_11:44:59_2018_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Wed_Sep_19_11:44:59_2018_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. 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 146 read successfully DEBUG:: there were 0 types with no dictionary 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 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 147 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 147 storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 147 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 148 read successfully DEBUG:: there were 0 types with no dictionary 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 storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 148 Sequence: ?EYTVITPGARTR Confidence: 1.0000 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_11:45:01_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. INFO:: 5 matched atoms had: mean devi: 0.0000 rms devi: 0.0000 max devi: 0.0000 min devi: 0.0000 INFO:: 5 matched atoms had: mean devi: 0.0121 rms devi: 0.0134 max devi: 0.0214 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0846 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1123 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0847 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0133 max devi: 0.0213 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.0002 rms devi: 0.0002 max devi: 0.0003 min devi: 0.0002 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3350 max devi: 0.5360 min devi: 0.0846 INFO:: 5 matched atoms had: mean devi: 0.2673 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1124 INFO:: 5 matched atoms had: mean devi: 0.0001 rms devi: 0.0001 max devi: 0.0001 min devi: 0.0001 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0134 max devi: 0.0214 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.0001 rms devi: 0.0001 max devi: 0.0001 min devi: 0.0001 INFO:: 5 matched atoms had: mean devi: 0.0120 rms devi: 0.0134 max devi: 0.0213 min devi: 0.0039 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.2703 rms devi: 0.3351 max devi: 0.5361 min devi: 0.0848 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_11:45:01_2018_modification_0.pdb.gz INFO:: Matching/moving molecule number 152 to 152 ERROR:: No symmetry available INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 0.1419 rms devi: 0.1486 max devi: 0.2431 min devi: 0.0283 INFO:: Axis orientation: ( 0.3864, -0.6781, -0.6252) INFO:: Rotation in CCP4 Polar Angles: Polar = (128.694,-60.3228,0.295209) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Wed_Sep_19_11:45:01_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 1, 0.003218, -0.003497| | -0.003225, 1, -0.001985| | 0.003491, 0.001997, 1| ( -24.05, -23.7, -24.44) No unit cell for this molecule, hence no fractional matrix. 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 153 read successfully DEBUG:: there were 0 types with no dictionary 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 154 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:: reference 153 has 750 atoms selected INFO:: moving 154 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_11:45:01_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% WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb se - new molecule by atom selection inherits shelx molecule flag PASS: new molecule by atom selection inherits shelx molecule flag Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy Entered testcase - Add water to SHELX molecule PASS: Add water to SHELX molecule Entered testcase - Find Waters for a SHELXL molecule PASS: Find Waters for a SHELXL molecule Entered testcase - NPD Anisotropic Atom [Mitch Miller] PASS: NPD Anisotropic Atom [Mitch Miller] Entered testcase - close shelx molecules PASS: close shelx molecules Entered testcase - Aniso Bs in P21 b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) PASS: Aniso Bs in P21 Entered testcase - Don't crash on reading a strange HAT file PASS: Don't crash on reading a strange HAT file Ended 02-shelx.scm Running 03-ligand.scm ... Entered testcase - Get monomer test PASS: Get monomer test Entered testcase - Delete all-molecule Hydrogens here 1 PASS: Delete all-molecule Hydrogens Entered testcase - Non-Autoloads PASS: Non-Autoloads Entered testcase - Move and Refine Ligand test PASS: Move and Refine Ligand test Entered testcase - Many Molecules - Ligand Fitting Fitting NPO gave these results: # PASS: Many Molecules - Ligand Fitting Entered testcase - flip residue (around eigen vectors) distance: 4.79714893189444 distance d2: 2.66560074985002e-7 PASS: flip residue (around eigen vectors) Entered testcase - Test dipole info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0) PASS: Test dipole Entered testcase - Reading new dictionary restraints replaces PASS: Reading new dictionary restraints replaces Entered testcase - Pyrogen Runs OK? PASS: Pyrogen Runs OK? Entered testcase - pyrogen dictionary does not make double-quoted atom names PASS: pyrogen dictionary does not make double-quoted atom names Ended 03-ligand.scm Running 04-cootaneer.scm ... Entered testcase - Assignment of new PIR sequence overwrites old assignment debug seq: ("A" . "ACDEFGHIKLMNPQ") PASS: Assignment of new PIR sequence overwrites old assignment Entered testcase - Cootaneer Beta Strand Cootaneering: imol 148 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" PASS: Cootaneer Beta Strand Ended 04-cootaneer.scm Running 05-rna-ghosts.scm ... Entered testcase - RNA NCS Ghosts There are 8 residues in chain "A" There are 8 residues in chain "B" PASS: RNA NCS Ghosts Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example PASS: SSM - Frank von Delft's Example Entered testcase - SSM - Alice Dawson's Example 0 "/home/paule/data/greg-data/tutorial-modern.pdb" 2 "/home/paule/data/greg-data/ins-code-fragment-pre.pdb" 3 "/home/paule/data/greg-data/tutorial-modern.pdb" 4 "PTR_from_dict" 5 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 6 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 7 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 8 "test-3hfl.map" 9 "/home/paule/data/greg-data/tutorial-modern.pdb" 10 "mainchain-forward" 11 "/home/paule/data/greg-data/tutorial-modern.pdb" 12 "mainchain-forwards" 13 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 14 "atom selection from tutorial-add-terminal-1-test.pdb" 15 "/home/paule/data/greg-data/frag-2wot.pdb" 16 "/home/paule/data/greg-data/tutorial-modern.pdb" 17 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 18 "sphere selection from tutorial-modern.pdb" 20 "/home/paule/data/greg-data/rotamer-test-fragment.pdb" 21 "/home/paule/data/greg-data/res098.pdb" 22 "/home/paule/data/greg-data/tutorial-modern.pdb" 23 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 24 "/home/paule/data/greg-data/pdb3knw.ent" 25 "/home/paule/data/greg-data/pdb1py3.ent" 28 "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb" 29 "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 32 "/home/paule/data/greg-data/tutorial-modern.pdb" 33 "atom selection from tutorial-modern.pdb" 34 "/home/paule/data/greg-data/tutorial-modern.pdb" 35 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 36 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 37 "/home/paule/data/greg-data/tutorial-modern.pdb" 38 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 39 "/home/paule/data/greg-data/tutorial-modern.pdb" 40 "/home/paule/data/greg-data/alt-conf-waters.pdb" 41 "/home/paule/data/greg-data/backrub-fragment.pdb" 42 "Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb" 43 "/home/paule/data/greg-data/coords-B3A.pdb" 44 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 45 "/home/paule/data/greg-data/test-TER-OXT.pdb" 46 "/home/paule/data/greg-data/val.pdb" 47 "/home/paule/data/greg-data/2yie-frag.pdb" 48 "/home/paule/data/greg-data/4f8g.pdb" 49 "/home/paule/data/greg-data/4f8g.pdb" 50 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 51 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 52 "/home/paule/data/greg-data/tutorial-modern.pdb" 53 "Generic Masked Map" 54 "difference-map" 57 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 58 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 59 "averaged-map" 60 "difference-map" 61 "/home/paule/data/greg-data/multi-carbo-coot-3.pdb" 62 "/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb" 63 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 64 "/home/paule/data/greg-data/monomer-VAL.pdb" 65 "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 66 "atom selection from tutorial-modern.pdb" 67 "/home/paule/data/greg-data/monomer-ACT.pdb" 68 "/home/paule/data/greg-data/tutorial-modern.pdb" 69 "/home/paule/data/greg-data/tutorial-modern.pdb" 70 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 71 "atom selection from tutorial-modern.pdb" 72 "/home/paule/data/greg-data/tutorial-modern.pdb" 73 "/home/paule/data/greg-data/tutorial-modern.pdb" 74 "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb" 75 "/home/paule/data/greg-data/tutorial-modern.pdb" 76 "/home/paule/data/greg-data/tutorial-modern.pdb" 77 "/home/paule/data/greg-data/pdb3hfl.ent" 78 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 79 "Ideal-A-form-RNA" 80 "Ideal-A-form-RNA" 81 "Ideal-A-form-DNA" 82 "Ideal-A-form-DNA" 83 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 84 "/home/paule/data/greg-data/some-waters-with-ter.pdb" 85 "/home/paule/data/greg-data/tm+some-waters.pdb" 86 "/home/paule/data/greg-data/tutorial-modern.pdb" 87 "/home/paule/data/greg-data/water-test-no-cell.pdb" 88 "/home/paule/data/greg-data/pathological-water-test.pdb" 89 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 90 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 91 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 92 "/home/paule/data/greg-data/tutorial-modern.pdb" 93 "/home/paule/data/greg-data/pdb1hvv.ent" 94 "/home/paule/data/greg-data/monomer-ACT.pdb" 95 "/home/paule/data/greg-data/monomer-NPO.pdb" 96 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_93" 97 "/home/paule/data/greg-data/tutorial-modern.pdb" 98 "atom selection from tutorial-modern.pdb" 99 "Copy_of_/home/paule/data/greg-data/tutorial-modernINFO:: 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 155 read successfully DEBUG:: there were 1 types with no dictionary 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 156 read successfully DEBUG:: there were 1 types with no dictionary INFO:: reference 155 has 169 atoms selected INFO:: moving 156 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_11:45:02_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% 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 157 read successfully 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:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 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:: 0.0520 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 5 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 158 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 no diffs NCS target chain has 93 peers. 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 163 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_11:45:03_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:03_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:03_2018_modification_2.pdb.gz 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: 163 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 163 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_11:45:03_2018_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Wed_Sep_19_11:45:03_2018_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 163 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 163 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_11:45:03_2018_modification_5.pdb.gz 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 164 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_11:45:03_2018_modification_0.pdb.gz 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" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 164 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 164 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_11:45:03_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Wed_Sep_19_11:45:03_2018_modification_2.pdb.gz 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 165 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 165 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:: Matching/moving molecule number 166 to 165 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_11:45:03_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) INFO:: Matching/moving molecule number 167 to 165 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: ( -0.431, 0.3986, 0.8095) INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Wed_Sep_19_11:45:03_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.6203, -0.2279, -0.7505| | -0.4559, -0.6739, 0.5814| | -0.6382, 0.7028, 0.3141| ( -22.14, -19.93, 1.626) INFO:: fractional coordinates matrix: | -0.8835, -0.09252, -0.543| | -0.5264, -0.4107, 0.8789| | -0.4875, 0.7087, 0.3141| ( -0.381, -0.2605, 0.01406) INFO:: Matching/moving molecule number 168 to 165 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: ( 0.6231, -0.7786, -0.07411) INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Wed_Sep_19_11:45:03_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) 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 169 read successfully DEBUG:: there were 0 types with no dictionary 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:: 0.0370 seconds to read MTZ file INFO:: 0.0240 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:: 0.0010 seconds for contour map INFO:: 0.0990 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 170 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 170 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 170 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 170 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 170 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 170 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 170 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 170 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 170 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 error (syntax error) error (syntax error) error (not syntax error) Traceback (most recent call last): File "", line 1, in NameError: name 'rr_not_found_thing' is not defined .pdb" 100 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 101 "/home/paule/data/greg-data/tutorial-modern.pdb" 102 "/home/paule/data/greg-data/pdb1py3.ent" 103 "/home/paule/data/greg-data/tutorial-modern.pdb" 104 "/home/paule/data/greg-data/tutorial-modern.pdb" 105 "/home/paule/data/greg-data/2goz-manip.pdb" 106 "/home/paule/data/greg-data/tutorial-modern.pdb" 107 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 108 "/home/paule/data/greg-data/HOF.RES" 109 "/home/paule/data/greg-data/hollander.ins" 112 "/home/paule/data/greg-data/insulin.fcf Diff-SigmaA" 113 "atom selection from insulin.res" 114 "atom selection from insulin.res" 116 "/home/paule/data/greg-data/horma-p21.res" 117 "new-horma.ins" 118 "/home/paule/data/greg-data/crash.hat" 119 "3GP_from_dict" 120 "/home/paule/data/greg-data/monomer-3GP.pdb" 121 "/home/paule/data/greg-data/test-LIG.pdb" 122 "/home/paule/data/greg-data/test-LIG.pdb" 123 "/home/paule/data/greg-data/monomer-3GP.pdb" 124 "/home/paule/data/greg-data/monomer-NPO.pdb" 125 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 126 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 127 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 128 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 129 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 130 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 131 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 132 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 133 "Masked (by protein)" 134 "Fitted ligand #0-0" 135 "Fitted ligand #1-0" 136 "Fitted ligand #2-0" 137 "Fitted ligand #3-0" 138 "Fitted ligand #4-0" 139 "Fitted ligand #5-0" 140 "Fitted ligand #6-0" 141 "Fitted ligand #7-0" 142 "Fitted ligand #8-0" 143 "Fitted ligand #9-0" 144 "/home/paule/data/greg-data/monomer-3GP.pdb" 145 "Copy_of_/home/paule/data/greg-data/monomer-3GP.pdb" 146 "/home/paule/data/greg-data/dipole-residues.pdb" 147 "/home/paule/data/greg-data/tutorial-modern.pdb" 148 "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb" 149 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 150 "Ideal-A-form-RNA" 153 "/home/paule/data/greg-data/1wly.pdb" 154 "/home/paule/data/greg-data/1yb5.pdb" PASS: SSM - Alice Dawson's Example Entered testcase - SSM by atom selection [JED Example] PASS: SSM by atom selection [JED Example] Ended 06-ssm.scm Running 07-ncs.scm ... Entered testcase - NCS maps test PASS: NCS maps test Entered testcase - NCS chains info NCS info: (("A" "B")) PASS: NCS chains info Entered testcase - NCS deviation info PASS: NCS deviation info Entered testcase - NCS Residue Range copy PASS: NCS Residue Range copy Entered testcase - NCS Residue Range edit to all chains result: (#t #t) PASS: NCS Residue Range edit to all chains Entered testcase - Manual NCS ghosts generates correct NCS chain ids NCS ghost chain IDs pre: (("B" "A" "C" "D")) NCS ghost chain IDs post: (("B" "A" "C" "D")) PASS: Manual NCS ghosts generates correct NCS chain ids Entered testcase - NCS maps overwrite existing maps ==== test-name: "Map 170 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 170 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 170 NCS found from matching Chain D onto Chain A" n-matchers: 2 PASS: NCS maps overwrite existing maps Ended 07-ncs.scm Running 08-utils.scm ... Entered testcase - Test key symbols WARNING:: could not find key-sym-code for "missing key" PASS: Test key symbols Entered testcase - Test running a Python function test_val_2 passed test_val_3 passed PASS: Test running a Python function Entered testcase - Internal/External Molecule Numbers match PASS: InternalINFO:: 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 179 read successfully DEBUG:: there were 0 types with no dictionary Entering test: OXT in restraints? INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/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 There are 2 data in /home/paule/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.1414 PASS: test symm trans to origin Entering test: test lsq plane LSQ deviations: 0.0000 0.0000 PASS: test lsq plane Entering test: test COO modification 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 INFO:: Reading coordinate file: /home/paule/data/greg-data/hideous-OXT.pdb PDB file /home/paule/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom created 7 bond restraints created 8 angle restraints created 1 plane restraints created 1 chiral vol restraints created 2 torsion restraints created 23 restraints INFO:: make_restraints(): made 13 non-bonded restraints initial distortion_score: 1241.5407 Initial RMS Z values bonds: 3.7208 angles: 7.4688 torsions: 0.2764 planes: 16.9011 non-bonded: 0.0000 chiral vol: 1.2266 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 243) at 0.0349 Final Estimated RMS Z Scores: bonds: 0.0017 angles: 0.0239 torsions: 0.1205 planes: 0.0019 non-bonded: 0.0000 chiral vol: 0.0068 rama plot: N/A start_pos: N/A GemanMcCl: N/A refinement_took 0.0050 seconds OXT out of plane distance: 0.0000 OXT->O distance: 2.1104 PASS: test COO modification Entering test: remove whitespace PASS: remove whitespace Entering test: New comp_ids are sane PASS: New comp_ids are sane Entering test: Remove Trailing Slash PASS: Remove Trailing Slash Entering test: Residues for phi,psi are close enough to be considered linked 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 bad residues for phi,psi calculation bad residues for phi,psi calculation PASS: Residues for phi,psi are close enough to be considered linked /External Molecule Numbers match Entered testcase - spacegroup operators to space group conversion PASS: spacegroup operators to space group conversion Ended 08-utils.scm Running 09-internal.scm ... Entered testcase - Test internal functions PASS: Test internal functions Ended 09-internal.scm === greg-tests Summary === # of testcases attempted 130 # of expected passes 129 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 1 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 Loading greg-tests/end.grg ... Loaded greg-tests/end.grg === Summary of all tests === # of tools 1 # of testcases attempted 130 # of expected passes 129 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 1 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 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:962): Gtk-WARNING **: cannot open display: test_coot: coot test failed