testing with greg testing with greg currently we are here: /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre Thu 2 Jan 17:08:09 GMT 2020 WARNING:: ccp4 setup file setup-ccp4 does not exist. /d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/ INFO:: Reading coordinate file: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /d/emsley/autobuild/install-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) ** (process:24008): WARNING **: 17:08:10.314: Widget is NULL: menubar1 WARNING:: remove_file_curlew_menu_item_maybe() ooops no menubar (use-graphics-interface-state) INFO:: coot.py imported Running python script /d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Afternoon Paul, Welcome to Coot version 0.8.9.3-pre (set-display-intro-string "Good Afternoon Paul, Welcome to Coot version 0.8.9.3-pre") (use-graphics-interface-state) Running python script /home/emsley/.coot-preferences/add_terminal_residue_working.py Running python script /home/emsley/.coot-preferences/contact_dots.py Running python script /home/emsley/.coot-preferences/coot_probe_dots.py Running python script /home/emsley/.coot-preferences/dragged_refinement.py Running python script /home/emsley/.coot-preferences/long_residues_refine.py Running python script /home/emsley/.coot-preferences/rama_plot.py Running python script /home/emsley/.coot-preferences/rotamer.py Running python script /home/emsley/.coot-preferences/startup.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good afternoon Paul. Welcome to Coot 0.8.9.3-pre") (set-display-lists-for-maps 0) load /home/emsley/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 1) (set-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 18.00) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) load /home/emsley/.coot-preferences/delete-sidechain-key.scm load /home/emsley/.coot-preferences/delete-sidechain-keybinding.scm load /home/emsley/.coot-preferences/h-bond-restraints.scm load /home/emsley/.coot-preferences/morph-residues-gui.scm load /home/emsley/.coot-preferences/pepflip-complicado.scm load /home/emsley/.coot-preferences/refine-utils.scm load /home/emsley/.coot-preferences/restraints.scm load /home/emsley/.coot-preferences/startup.scm (set-display-lists-for-maps 0) load /home/emsley/.coot-preferences/template-key-bindings.scm (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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/emsley/data/greg-data/2WF6.cif mmCIF file /home/emsley/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/emsley/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/emsley/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_emsley_data_greg-data_ins-code-fragment-pre.pdb_Thu_Jan__2_17:08:10_2020_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Thu_Jan__2_17:08:10_2020_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Thu_Jan__2_17:08:10_2020_modification_2.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_Thu_Jan__2_17:08:10_2020_modification_0.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_modification_1.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_modification_2.pdb.gz INFO:: Matching/moving molecule number 4 to 3 INFO:: LSQ matched 15 atoms INFO:: 15 matched atoms had: mean devi: 0.577852 rms devi: 0.627183 max devi: 0.94351 min devi: 0.276538 INFO:: Axis orientation: ( 0.746, -0.01099, -0.6659) INFO:: Rotation in CCP4 Polar Angles: Polar = (131.748,-0.84427,52.3113) INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_modification_3.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8276, 0.5237, -0.2017| | -0.5301, 0.6114, -0.5875| | -0.1843, 0.5932, 0.7837| ( 19.67, 35.56, 6.621) No unit cell for this molecule, hence no fractional matrix. INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_modification_4.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 WARNING:: in torsion match() quad moving not all non-blank ------ after matching, check the torsions torsion check: ( N CA CB CG ) was 65.41 should be -47.18 and is -47.18 torsion check: ( CA CB CG CD2) was 71.13 should be -56.84 and is -56.84 torsion check: ( O C CA CB ) was -63.23 should be -44.77 and is -44.77 INFO:: rotated 3 torsions in matching torsions INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:10_2020_modification_0.pdb.gz ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] [spec: 1 "A" 101 ""] INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:10_2020_modification_1.pdb.gz DEBUG:: In copy_mol_and_refine() refine range: chain :A: 86 :: 86 :: altconf "" coords mol: 3 map mol: -1 INFO:: created 39 restraints created 16 bond restraints created 22 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: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 706 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 211900.15 Initial RMS Z values bonds: 12.79 angles: 9.70 torsions: N/A planes: 12.47 non-bonded: 290.63 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at 118.66 Final Estimated RMS Z Scores: bonds: 0.09 angles: 1.94 torsions: N/A planes: 1.03 non-bonded: 0.00 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 0.00 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:10_2020_modification_2.pdb.gz INFO:: replace_coords: 16 atoms updated. WARNING:: Error reading bogus.map Read map bogus.map failed WARNING:: Can't find file bogus.mtz INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.60 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.03 seconds to read MTZ file INFO:: 0.05 seconds to initialize map INFO:: 0.05 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.12 Map minimum: ..... -0.91 INFO:: 0.00 seconds for contour map INFO:: 0.14 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/emsley/data/greg-data/broken.mtz INFO:: not an mtz file: /home/emsley/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.60 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.02 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.05 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 3.12 Map minimum: ..... -0.91 INFO:: 0.00 seconds for contour map INFO:: 0.08 seconds in total INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz INFO:: Number of observed reflections: 17920 INFO:: finding ASU unique map points with sampling rate 2.60 INFO:: grid sampling...Nuvw = ( 108, 160, 162) INFO:: 0.02 seconds to read MTZ file INFO:: 0.03 seconds to initialize map INFO:: 0.04 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.26 Map maximum: ..... 1.78 Map minimum: ..... -1.03 INFO:: 0.00 seconds for contour map INFO:: 0.10 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: -1.03, max: 1.78 -1.00 7 -0.93 41 -0.86 191 -0.78 586 -0.71 1746 -0.64 4206 -0.57 9248 -0.50 17586 -0.43 29941 -0.36 45756 -0.29 67360 -0.22 97280 -0.15 143881 -0.08 199949 -0.01 227160 0.06 192478 0.13 118867 0.20 62666 0.27 36677 0.34 27550 0.41 23779 0.48 20707 0.55 18091 0.62 15228 0.69 12099 0.76 9240 0.83 6657 0.90 4375 0.97 2822 1.05 1624 1.12 867 1.19 461 1.26 237 1.33 130 1.40 83 1.47 49 1.54 23 1.61 18 1.68 9 1.75 5 1.82 0 INFO:: n grid points: 1399680 INFO:: mean before filtering: 0.00 INFO:: variance before filtering: 0.07 INFO:: filter by ignoring 995 of 1399680 counts ( = 0.0711%) with values around 0.0065 from bin 3685 of 10000 Map mean: ........ -0.0000 Map rmsd: ........ 0.2605 Map maximum: ..... 1.7844 Map minimum: ..... -1.0312 WARNING:: Error reading . . is a directory. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /d/emsley/autobuild/install-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: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i40.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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:12_2020_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:24008): Gtk-CRITICAL **: 17:08:13.057: IA__gtk_widget_show: assertion 'GTK_IS_WIDGET (widget)' failed INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:13_2020_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:13_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0330 seconds to read MTZ file INFO:: 0.0020 seconds to initialize map INFO:: 0.0560 seconds for FFT INFO:: 0.0080 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.1010 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 ------------------ add_view_raw() B11 View INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:13_2020_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:13_2020_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:13_2020_modification_2.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/rotamer-test-fragment.pdb PDB file /home/emsley/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 ""] INFO:: Reading coordinate file: /home/emsley/data/greg-data/eleanor-HIS.pdb PDB file /home/emsley/data/greg-data/eleanor-HIS.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 21 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/res098.pdb PDB file /home/emsley/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary DEBUG:: In copy_mol_and_refine() refine range: chain :X: 15 :: 15 :: altconf "" coords mol: 22 map mol: -1 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 128 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2951.2431 Initial RMS Z values bonds: 0.8732 angles: 1.0078 torsions: N/A planes: 0.5766 non-bonded: 22.6696 chiral vol: 0.3851 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 10) at 1603.0629 Final Estimated RMS Z Scores: bonds: 4.5730 angles: 3.3091 torsions: N/A planes: 1.8776 non-bonded: 8.9511 chiral vol: 0.7470 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 2.9090 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_res098.pdb_Thu_Jan__2_17:08:14_2020_modification_0.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 23 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0440 seconds to read MTZ file INFO:: 0.0040 seconds to initialize map INFO:: 0.0690 seconds for FFT INFO:: 0.0100 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.1290 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:15_2020_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! ------------------- INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:15_2020_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 12.1008 Good afternoon Paul Emsley. Welcome to Coot 0.8.9.3-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 debug:: in overlap-by-main-chain:: ---------------- imol-mov: 4 imol-ref: 3 DEBUG:: ------ new-chain-id-info: (1 ((#t "A" 101 ""))) DEBUG:: ------ merge-status: 1 debug:: ------ new-res-spec: (#t "A" 101 "") debug:: ------ change-residue-number to 86 debug:: ------ chain ids : "A" "A" C-N dist good enough: 1.33847240473201 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 0.311500996351242 #f PASS: Map Sigma Entered testcase - Another Level Test PASS: Another Level Test Entered testcase - Sharpen map from map PASS: Sharpen map from map Entered testcase - 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 dd-1: 0.0 dd-2: 2.36045066887977 PASS: 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 rotamINFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3knw.ent PDB file /home/emsley/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links 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 25 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3knw.ent_Thu_Jan__2_17:08:15_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links 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 26 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_emsley_data_greg-data_pdb1py3.ent_Thu_Jan__2_17:08:15_2020_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 er on alt-confed residue Entered testcase - Rotamers work on MSE se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746)) se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616)) PASS: Rotamers work on MSE Entered testcase - 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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 27 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0280 seconds to read MTZ file INFO:: 0.0020 seconds to initialize map INFO:: 0.0510 seconds for FFT INFO:: 0.0080 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.0910 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:15_2020_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/emsley/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 29 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-pepflip-test.pdb_Thu_Jan__2_17:08:15_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 ------------------ add_view_raw() CIS-TRANS cispep View omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_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_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_2.pdb.gz DEBUG:: ================ refine_residue_range: 30 A 11:: 12:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 11 :: 12 :: altconf "" coords mol: 30 map mol: 5 debug:: in refine_residues_vec() with altconf "" 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 137 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 6702.4094 Initial RMS Z values bonds: 14.8983 angles: 8.7656 torsions: N/A planes: 3.4883 non-bonded: 41.0829 chiral vol: 3.2117 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -3111.9438 Final Estimated RMS Z Scores: bonds: 3.7624 angles: 2.2634 torsions: N/A planes: 2.5430 non-bonded: 10.2967 chiral vol: 0.7311 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.1620 Refinement elapsed time: 0.1780 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.7591 DEBUG:: ================ refine_residue_range: 30 A 11:: 12:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 11 :: 12 :: altconf "" coords mol: 30 map mol: 5 debug:: in refine_residues_vec() with altconf "" 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 221 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -4219.2183 Initial RMS Z values bonds: 3.5118 angles: 2.4494 torsions: N/A planes: 2.7241 non-bonded: 6.8639 chiral vol: 0.8372 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -4391.6571 Final Estimated RMS Z Scores: bonds: 3.2832 angles: 2.0277 torsions: N/A planes: 2.6195 non-bonded: 6.3741 chiral vol: 0.5811 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.3580 Refinement elapsed time: 0.1150 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 31 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:16_2020_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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 33 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:16_2020_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_Thu_Jan__2_17:08:16_2020_modification_1.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 35 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0470 seconds for FFT INFO:: 0.0080 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.0820 seconds in total DEBUG:: ================ refine_residue_range: 35 B 72:: 72:: :B: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :B: 72 :: 72 :: altconf "B" coords mol: 35 map mol: 36 debug:: in refine_residues_vec() with altconf "B" INFO:: created 10 restraints created 5 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 64 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -2362.5539 Initial RMS Z values bonds: 2.9785 angles: 1.3074 torsions: N/A planes: 0.6113 non-bonded: 0.8668 chiral vol: 0.8558 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -2507.9378 Final Estimated RMS Z Scores: bonds: 0.7572 angles: 0.8546 torsions: N/A planes: 0.4816 non-bonded: 0.0779 chiral vol: 0.5526 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.7430 Refinement elapsed time: 0.1530 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:16_2020_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 37 read successfully DEBUG:: there were 0 types with no dictionary DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:16_2020_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" debug:: in refine_residues_vec() with altconf "" INFO:: created 81 restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints 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: -15850.1474 Initial RMS Z values bonds: 2.6203 angles: 1.5627 torsions: N/A planes: 0.8383 non-bonded: 0.0007 chiral vol: 0.6412 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -16343.7575 Final Estimated RMS Z Scores: bonds: 1.0276 angles: 0.7800 torsions: N/A planes: 0.6346 non-bonded: 0.0000 chiral vol: 0.1566 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.1210 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:16_2020_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. debug:: in refine_residues_vec() with altconf "" INFO:: created 84 restraints created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints 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: -7240.6588 Initial RMS Z values bonds: 2.1848 angles: 1.4708 torsions: N/A planes: 1.7875 non-bonded: 5.2955 chiral vol: 10.5313 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -15861.6327 Final Estimated RMS Z Scores: bonds: 1.5657 angles: 2.0166 torsions: N/A planes: 1.9124 non-bonded: 0.0735 chiral vol: 1.2451 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.7640 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:16_2020_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 38 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0460 seconds for FFT INFO:: 0.0080 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.0810 seconds in total DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 40 :: 43 :: altconf "" coords mol: 38 map mol: 39 debug:: in refine_residues_vec() with altconf "" INFO:: created 67 restraints created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints 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: -3045.0595 Initial RMS Z values bonds: 2.0802 angles: 1.5577 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.7704 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -11482.4822 Final Estimated RMS Z Scores: bonds: 1.6070 angles: 2.2751 torsions: N/A planes: 2.0946 non-bonded: 0.0963 chiral vol: 1.4573 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.2150 Refinement elapsed time: 1.3190 DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 40 :: 43 :: altconf "" coords mol: 38 map mol: 39 debug:: in refine_residues_vec() with altconf "" ---------------------------------------------- ---------------------------------------------- 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 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: 4736.2655 Initial RMS Z values bonds: 2.0802 angles: 1.5577 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.7704 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -3096.1965 Final Estimated RMS Z Scores: bonds: 0.6605 angles: 1.6575 torsions: N/A planes: 2.2513 non-bonded: 0.0350 chiral vol: 0.7040 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 10.6730 Refinement elapsed time: 2.4580 DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 40 :: 43 :: altconf "" coords mol: 38 map mol: 39 debug:: in refine_residues_vec() with altconf "" ---------------------------------------------- ---------------------------------------------- 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 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: 6082.7324 Initial RMS Z values bonds: 2.0802 angles: 1.5577 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.7704 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -1687.9568 Final Estimated RMS Z Scores: bonds: 0.4814 angles: 1.4444 torsions: N/A planes: 2.1530 non-bonded: 0.0218 chiral vol: 0.5373 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 21.9080 Refinement elapsed time: 11.2340 DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 40 :: 43 :: altconf "" coords mol: 38 map mol: 39 debug:: in refine_residues_vec() with altconf "" ---------------------------------------------- ---------------------------------------------- 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 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: 6537.2933 Initial RMS Z values bonds: 2.0802 angles: 1.5577 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.7704 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -1179.0725 Final Estimated RMS Z Scores: bonds: 0.3794 angles: 1.2107 torsions: N/A planes: 1.9961 non-bonded: 0.0103 chiral vol: 0.5195 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 23.5970 Refinement elapsed time: 1.6890 INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 40 read successfully DEBUG:: there were 0 types with no dictionary debug:: in refine_residues_vec() with altconf "" ---------------------------------------------- ---------------------------------------------- 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 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: -1608.3783 Initial RMS Z values bonds: 2.6094 angles: 1.4906 torsions: N/A planes: 0.7374 non-bonded: 0.0256 chiral vol: 0.8303 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -1917.2396 Final Estimated RMS Z Scores: bonds: 0.1670 angles: 0.7090 torsions: N/A planes: 0.4424 non-bonded: 0.0032 chiral vol: 0.3186 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 24.1340 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:35_2020_modification_0.pdb.gz INFO:: replace_coords: 27 atoms updated. 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=0.279831287906342 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.31073682992 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 1.607" 1.6069860458374) ("Angles" "Angles: 2.275" 2.27508354187012) ("Planes" "Planes: 2.095" 2.09464716911316) ("Non-bonded" "Non-bonded: 0.310" 0.310280948877335) ("Chirals" "Chirals: 1.457" 1.45725882053375))) ow factor: 1.85849389433861 INFO:: setting refinement weight to 17.371166104535 refinement results: ("" 0 (("Bonds" "Bonds: 0.661" 0.660505056381226) ("Angles" "Angles: 1.658" 1.65754890441895) ("Planes" "Planes: 2.251" 2.25134062767029) ("Non-bonded" "Non-bonded: 0.187" 0.187022611498833) ("Chirals" "Chirals: 0.704" 0.703979432582855))) ow factor: 1.31834350526333 INFO:: setting refinement weight to 9.99474706905847 refinement results: ("" 0 (("Bonds" "Bonds: 0.481" 0.481422454118729) ("Angles" "Angles: 1.444" 1.44444286823273) ("Planes" "Planes: 2.153" 2.15304064750671) ("Non-bonded" "Non-bonded: 0.148" 0.147786349058151) ("Chirals" "Chirals: 0.537" 0.537297546863556))) ow factor: 1.15405087918043 INFO:: setting refinement weight to 7.50450238272587 refinement results: ("" 0 (("Bonds" "Bonds: 0.379" 0.379440784454346) ("Angles" "Angles: 1.211" 1.21067309379578) ("Planes" "Planes: 1.996" 1.99607837200165) ("Non-bonded" "Non-bonded: 0.101" 0.101409189403057) ("Chirals" "Chirals: 0.520" 0.519510805606842))) ow factor: 1.02642576396465 PASS: Refinement gives useful results Entered testcase - Neighbour-Refine doesn't destroy disulfide bonds bond-length-within-tolerance? bond-length 2.03197508776284 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6101188659668 27.522180557251 11.2309684753418)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7754211425781 27.0276489257812 9.44557189941406)) debug:: in refine_residues_vec() with altconf "" INFO:: created 52 restraints created 23 bond restraints created 25 angle restraints created 0 plane restraints created 4 chiral vol restraints 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 763 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -1917.2396 Initial RMS Z values bonds: 0.1670 angles: 0.7090 torsions: N/A planes: 0.4424 non-bonded: 0.0032 chiral vol: 0.3186 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -1917.2423 Final Estimated RMS Z Scores: bonds: 0.1674 angles: 0.7089 torsions: N/A planes: 0.4426 non-bonded: 0.0032 chiral vol: 0.3183 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 24.1840 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:35_2020_modification_1.pdb.gz INFO:: replace_coords: 27 atoms updated. bond-length-within-tolerance? bond-length 2.03197644083519 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6100997924805 27.5221691131592 11.2309703826904)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.775426864624 27.0276279449463 9.44556331634521)) INFO:: Reading coordinate file: /home/emsley/data/greg-data/alt-conf-waters.pdb PDB file /home/emsley/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 41 read successfully DEBUG:: there were 0 types with no dictionary DEBUG:: ================ refine_residue_range: 41 D 71:: 71:: :A: 1 masking....masking done INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-waters.pdb_Thu_Jan__2_17:08:35_2020_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: Reading coordinate file: /home/emsley/data/greg-data/backrub-fragment.pdb PDB file /home/emsley/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 42 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Thu_Jan__2_17:08:35_2020_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Thu_Jan__2_17:08:35_2020_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/coords-B3A.pdb PDB file /home/emsley/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 44 read successfully DEBUG:: there were 1 types with no dictionary DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 44 map mol: -1 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 7) at 0.0001 Final Estimated RMS Z Scores: bonds: 0.0011 angles: 0.0034 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0000 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 24.4750 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Thu_Jan__2_17:08:36_2020_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/lib-B3A.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/lib-B3A.cif had no bond restraints DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 44 map mol: -1 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: 0.0001 Initial RMS Z values bonds: 0.0011 angles: 0.0034 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0000 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: 0.0014 angles: 0.0027 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0003 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 24.6050 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Thu_Jan__2_17:08:36_2020_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. Welcome to Coot DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 44 map mol: -1 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: 3.0104 Initial RMS Z values bonds: 0.6699 angles: 0.3748 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.2531 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at 0.0001 Final Estimated RMS Z Scores: bonds: 0.0012 angles: 0.0041 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0010 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 24.7180 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Thu_Jan__2_17:08:36_2020_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0250 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0470 seconds for FFT INFO:: 0.0070 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.0820 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-TER-OXT.pdb PDB file /home/emsley/data/greg-data/test-TER-OXT.pdb has been read. 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:: backup file coot-backup/_home_emsley_data_greg-data_test-TER-OXT.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/val.pdb PDB file /home/emsley/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 47 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_home_emsley_data_greg-data_val.pdb_Thu_Jan__2_17:08:36_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/2yie-frag.pdb PDB file /home/emsley/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 48 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_2yie-frag.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 49 read successfully DEBUG:: there were 1 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 50 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0020 seconds to initialize map INFO:: 0.0470 seconds for FFT INFO:: 0.0080 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.0830 seconds in total INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2000 INFO:: grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.0230 seconds to read MTZ file INFO:: 0.0290 seconds to initialize map INFO:: 0.0300 seconds for FFT INFO:: 0.0050 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:: 0.0880 seconds in total INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 53 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.0014 st.d: 0.3056 Map statistics: min: -0.9116, max: 3.1176 -0.8613 21 -0.7605 144 -0.6598 1355 -0.5591 8283 -0.4583 34328 -0.3576 88827 -0.2569 140726 -0.1562 185091 -0.0554 222101 0.0453 222174 0.1460 111281 0.2468 50680 0.3475 29724 0.4482 22854 0.5490 19216 0.6497 16308 0.7504 13864 0.8512 11002 0.9519 8557 1.0526 6028 1.1534 4257 1.2541 2950 1.3548 1917 1.4555 1136 1.5563 670 1.6570 352 1.7577 210 1.8585 91 1.9592 24 2.0599 14 2.1607 7 2.2614 8 2.3621 7 2.4629 8 2.5636 2 2.6643 2 2.7650 3 2.8658 0 2.9665 1 3.0672 0 3.1680 1 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: (0.992907404899597 0.960582137107849 0.99147617816925 0.666360557079315 0.677083969116211 0.822775840759277 0.746499538421631 1.12646055221558 1.03679931163788 1.02070951461792 0.81580126285553) 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: 0.0602 Map statistics: min: -3.0391, max: 0.7582 -2.9917 2 -2.8967 1 -2.8018 2 -2.7069 2 -2.6119 4 -2.5170 5 -2.4221 3 -2.3271 4 -2.2322 9 -2.1373 5 -2.0423 3 -1.9474 11 -1.8525 7 -1.7575 10 -1.6626 27 -1.5677 17 -1.4727 51 -1.3778 80 -1.2829 105 -1.1879 157 -1.0930 184 -0.9981 302 -0.9031 394 -0.8082 517 -0.7133 579 -0.6184 639 -0.5234 839 -0.4285 934 -0.3336 1114 -0.2386 1318 -0.1437 1755 -0.0488 339081 0.0462 845092 0.1411 3721 0.2360 3127 0.3310 2324 0.4259 1272 0.5208 410 0.6158 95 0.7107 21 0.8056 1 diff-high-values: (0.00614375341683626 0.00179204856976867 0.00554320681840181 0.00859612133353949 0.00364016066305339 0.00399892218410969 0.00163731398060918 0.00837583001703024 0.00694983452558517 0.00368036120198667 0.0069606532342732) diff-low-values: (-0.908486723899841 -0.95145583152771 -1.25011610984802 -1.226642370224 -1.11153709888458 -0.85110729932785 -0.853124260902405 -0.707162618637085 -0.954133033752441 -0.566797137260437) INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 56 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0460 seconds for FFT INFO:: 0.0080 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0020 seconds for contour map INFO:: 0.0800 seconds in total INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.6000 INFO:: grid sampling...Nuvw = ( 192, 224, 112) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0450 seconds for FFT INFO:: 0.0080 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.1176 Map minimum: ..... -0.9116 INFO:: 0.0010 seconds for contour map INFO:: 0.0790 seconds in total INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5000 INFO:: grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0410 seconds to initialize map INFO:: 0.0420 seconds for FFT INFO:: 0.0060 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:: 0.1150 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 192, 224, 112) 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: -0.9080, max: 3.1098 -0.8578 23 -0.7573 157 -0.6569 1462 -0.5564 8793 -0.4560 36076 -0.3555 91860 -0.2551 144385 -0.1547 189058 -0.0542 225530 0.0462 197979 0.1467 112236 0.2471 51757 0.3476 30773 0.4480 23747 0.5484 20007 0.6489 16994 0.7493 14466 0.8498 11446 0.9502 8941 1.0507 6285 1.1511 4436 1.2516 3081 1.3520 2004 1.4524 1203 1.5529 697 1.6533 376 1.7538 224 1.8542 97 1.9547 38 2.0551 16 2.1555 13 2.2560 17 2.3564 13 2.4569 11 2.5573 6 2.6578 6 2.7582 4 2.8587 3 2.9591 2 3.0595 1 3.1600 1 Map statistics: mean: 0.0000 st.d: 0.0011 Map statistics: min: -0.0111, max: 0.0150 -0.0108 1 -0.0101 1 -0.0095 3 -0.0088 1 -0.0082 2 -0.0075 9 -0.0068 27 -0.0062 93 -0.0055 244 -0.0049 747 -0.0042 1999 -0.0036 4699 -0.0029 10741 -0.0023 24133 -0.0016 56083 -0.0010 150373 -0.0003 369547 0.0003 357690 0.0010 134126 0.0016 47222 0.0023 21496 0.0029 11213 0.0036 6131 0.0043 3424 0.0049 1958 0.0056 1091 0.0062 557 0.0069 329 0.0075 154 0.0082 60 0.0088 30 0.0095 15 0.0101 5 0.0108 7 0.0114 2 0.0121 4 0.0127 3 0.0134 2 0.0141 0 0.0147 2 0.0154 0 INFO:: Reading coordinate file: /home/emsley/data/greg-data/multi-carbo-coot-3.pdb PDB file /home/emsley/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 62 read successfully DEBUG:: there were 2 types with no dictionary DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 2 :: altconf "" coords mol: 62 map mol: -1 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): 27.0880 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_multi-carbo-coot-3.pdb_Thu_Jan__2_17:08:38_2020_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. PASS: Mask and difference map Entered testcase - Skeletonize a map PASS: Skeletonize a map Entered testcase - Simple Averaged maps INFO:: map sigmas: normal 0.311070144176483 and diff-map: 0.00108510116115212 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/emsley/data/greg-data/pdb2qc1-sans-cho.pdb PDB file /home/emsley/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 63 read successfully DEBUG:: there were 1 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0230 seconds to read MTZ file INFO:: 0.0100 seconds to initialize map INFO:: 0.0150 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 ......... checking for /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab ..that failed - trying /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/NAG-decorations.tab INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_1.pdb.gz INFO:: link torsion generated from link bond restraint INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_2.pdb.gz INFO:: replace_coords: 22 atoms updated. debug:: in refine_residues_vec() with altconf "" 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 3 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: 61627.5852 Initial RMS Z values bonds: 1.0337 angles: 3.2356 torsions: N/A planes: 6.9590 non-bonded: 87.9889 chiral vol: 0.3636 rama plot: N/A start_pos: N/A GemanMcCl: N/A INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. debug:: in refine_residues_vec() with altconf "" 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 3 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 451 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 19857.6554 Initial RMS Z values bonds: 0.4642 angles: 1.0934 torsions: N/A planes: 0.7818 non-bonded: 44.8200 chiral vol: 0.4827 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -489.0507 Final Estimated RMS Z Scores: bonds: 0.4320 angles: 0.9119 torsions: N/A planes: 0.8150 non-bonded: 0.0022 chiral vol: 0.5075 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 49.1210 INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. PASS: Make a glycosidic linkage Entered testcase - Refine an NAG-ASN Link bond-length-within-tolerance? bond-length 1.43597463820273 with target 1.43 and tolerance 0.2 for atom ((" ND2" "") (1.0 16.9300003051758 " N" "") (-15.001612663269 -0.467886626720428 -7.01484489440918)) is ((" C1 " "") (1.0 45.0 " C" "") (-14.0559310913086 -0.695992231369019 -5.95858860015869)) INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-VAL.pdb PDB file /home/emsley/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 65 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 1 CB DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 65 map mol: -1 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: 21.7281 Initial RMS Z values bonds: 0.7365 angles: 0.7519 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0277 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 3) at 0.0153 Final Estimated RMS Z Scores: bonds: 0.0019 angles: 0.0238 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0322 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 49.2230 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 65 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_0.pdb.gz PDB file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_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 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 65 map mol: -1 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: 21.7281 Initial RMS Z values bonds: 0.7365 angles: 0.7519 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0277 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 3) at 0.0153 Final Estimated RMS Z Scores: bonds: 0.0019 angles: 0.0238 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0322 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 49.3250 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. PASS: Refine an NAG-ASN Link Entered testcase - Test for flying hydrogens on undo bond-length-within-tolerance? bond-length 0.972985777356827 with target 0.96 and tolerance 0.02 for atom (("HG11" "") (1.0 20.0 " H" "") (3.48122096061707 -0.187875345349312 -1.98467183113098)) is ((" CG1" "") (1.0 20.0 " C" "") (2.8759868144989 -0.203856721520424 -1.2230042219162)) INFO:: Reading coordinate file: /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. 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 66 read successfully DEBUG:: there were 0 types with no dictionary DEBUG:: In copy_mol_and_refine() refine range: chain :B: 6 :: 6 :: altconf "" coords mol: 66 map mol: -1 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: 2263.3054 Initial RMS Z values bonds: 7.1303 angles: 6.7178 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0334 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 5) at 0.0469 Final Estimated RMS Z Scores: bonds: 0.0022 angles: 0.0379 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0489 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 49.4310 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Thu_Jan__2_17:09:01_2020_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. 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 0.973010154757159 with target 0.96 and tolerance 0.02 for atom (("HD11" "") (1.0 10.5299997329712 " H" "") (-10.1254034042358 6.53209161758423 7.00641536712646)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1308145523071 5.64076614379883 6.61621236801147)) bond-length-within-tolerance? bond-length 0.972997348417048 with target 0.96 and tolerance 0.02 for atom (("HD12" "") (1.0 10.1300001144409 " H" "") (-9.76907539367676 5.68026351928711 5.71382188796997)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1308145523071 5.64076614379883 6.61621236801147)) bond-length-within-tolerance? bond-length 0.972972386005099 with target 0.96 and tolerance 0.02 for atom (("HD13" "") (1.0 10.5600004196167 " H" "") (-11.0441112518311 5.30675506591797 6.58457374572754)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1308145523071 5.64076614379883 6.61621236801147)) bond-length-within-tolerance? bond-length 0.972992004194165 with target 0.96 and tolerance 0.02 for atom (("HD21" "") (1.0 10.1499996185303 " H" "") (-7.98362302780151 3.13911032676697 7.13967418670654)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55780792236328 3.69762277603149 6.58732557296753)) bond-length-within-tolerance? bond-length 0.973016117814419 with target 0.96 and tolerance 0.02 for atom (("HD22" "") (1.0 10.3000001907349 " H" "") (-9.21132946014404 3.13903474807739 6.13163995742798)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55780792236328 3.69762277603149 6.58732557296753)) bond-length-within-tolerance? bond-length 0.97300876474718 with target 0.96 and tolerance 0.02 for atom (("HD23" "") (1.0 10.6499996185303 " H" "") (-8.01666164398193 4.16603326797485 5.92816066741943)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55780792236328 3.69762277603149 6.58732557296753)) DEBUG:: ================ refine_residue_range: 67 A 30:: 30:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 30 :: 30 :: altconf "" coords mol: 67 map mol: 5 debug:: in refine_residues_vec() with altconf "" 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: 2760.1885 Initial RMS Z values bonds: 2.7809 angles: 1.0747 torsions: N/A planes: 3.0558 non-bonded: 79.8585 chiral vol: 1.1767 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -492.4876 Final Estimated RMS Z Scores: bonds: 0.2639 angles: 0.2999 torsions: N/A planes: 0.3241 non-bonded: 0.0214 chiral vol: 0.0559 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 49.8850 Refinement elapsed time: 0.3910 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:09:01_2020_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. 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: 2.62147952908895: bond-length-within-tolerance? bond-length 2.62147952908895 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.3067474365234 4.49700593948364 19.8036155700684)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.5366897583008 6.70065450668335 19.0941581726074)) DEBUG:: ================ refine_residue_range: 67 A 30:: 30:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 30 :: 30 :: altconf "" coords mol: 67 map mol: 5 debug:: in refine_residues_vec() with altconf "" 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: 11905.0124 Initial RMS Z values bonds: 32.1444 angles: 0.2999 torsions: N/A planes: 0.3241 non-bonded: 0.0000 chiral vol: 0.0559 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -544.8533 Final Estimated RMS Z Scores: bonds: 0.0765 angles: 0.1076 torsions: N/A planes: 0.3525 non-bonded: 0.0000 chiral vol: 0.0750 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 50.1290 Refinement elapsed time: 0.2250 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:09:01_2020_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.50860713059272: bond-length-within-tolerance? bond-length 1.50860713059272 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5384674072266 4.9270167350769 19.3901653289795)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.2881469726563 6.20275497436523 19.0962810516357)) INFO:: wrote mmCIF "coot-test-ala.cif" INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 68 read successfully DEBUG:: there were 1 types with no dictionary Welcome to Coot WARNING:: bond_restraint_length 4 should be 5 DEBUG:: ================ refine_residue_range: 68 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 68 map mol: 5 debug:: in refine_residues_vec() with altconf "" 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: 4838.0256 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 Refinement elapsed time: 0.9380 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-ACT.pdb_Thu_Jan__2_17:09:02_2020_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_2.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_3.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_6.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_7.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 70 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 in new_molecule_by_residue_type_selection Something bad happened - No residues selected in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 74 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/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 50/87 Molecule 75 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 75 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/emsley/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_emsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Thu_Jan__2_17:09:03_2020_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: 202615928 "A" 1 ""] -> ASP [spec: 202615928 "A" 2 ""] -> VAL [spec: 202615928 "A" 3 ""] -> SER [spec: 202615928 "A" 11 ""] -> LEU [spec: 202615928 "A" 12 ""] -> PRO [spec: 202615928 "A" 13 ""] -> PRO [spec: 202615928 "A" 62 ""] -> PRO [spec: 202615928 "A" 63 ""] -> GLY Deletions: [spec: 202615928 "A" 25 ""] [spec: 202615928 "A" 34 ""] Mutations: [spec: 202615928 "A" 24 ""] -> SER [spec: 202615928 "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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 77 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3hfl.ent PDB file /home/emsley/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 78 read successfully DEBUG:: there were 1 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz INFO:: Number of observed reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.0180 seconds to read MTZ file INFO:: 0.0050 seconds to initialize map INFO:: 0.0120 seconds for FFT INFO:: 0.0020 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:: 0.0370 seconds in total INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.8340 INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/some-waters-with-ter.pdb PDB file /home/emsley/data/greg-data/some-waters-with-ter.pdb has been read. 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 85 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_some-waters-with-ter.pdb_Thu_Jan__2_17:09:04_2020_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/emsley/data/greg-data/tm+some-waters.pdb PDB file /home/emsley/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: 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 = ( 59.88, 2.985, -4.28) is too big to be water INFO:: cluster at xyz = ( 70.02, 19.06, 18.65) is too big to be water INFO:: cluster at xyz = ( 53.05, 9.039, 20.15) is too big to be water INFO:: found 61 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tm+some-waters.pdb_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 87 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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/emsley/data/greg-data/water-test-no-cell.pdb PDB file /home/emsley/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 88 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_water-test-no-cell.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /home/emsley/data/greg-data/pathological-water-test.pdb PDB file /home/emsley/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 89 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_pathological-water-test.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0230 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0170 seconds for FFT INFO:: 0.0010 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:: 0.0420 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:07_2020_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: 92 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 92 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 93 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/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 94 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 95 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 96 read successfully DEBUG:: there were 1 types with no dictionary ------- resulting_merge_info has size 2 -------- resulting_merge_info[0] {residue-spec-not-set} -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" ------- resulting_merge_info has size 6 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 98 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_modification_0.pdb.gz ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_modification_1.pdb.gz ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Matching/moving molecule number 101 to 100 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_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 ::::: (75 "A" 1 "") #f #f ::::: (75 "A" 4 "") #t #t ::::: (75 "A" 57 "") #t #t ::::: (75 "A" 60 "") #f #f ::::: (75 "A" 61 "") #f #f ::::: (75 "A" 92 "") #t #t ::::: (75 "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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 102 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links 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 103 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 102 to 103 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 105 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/2goz-manip.pdb PDB file /home/emsley/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 10/85 Molecule 106 read successfully DEBUG:: there were 7 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 107 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0160 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:: 0.0430 seconds in total masking....masking done INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_modification_0.pdb.gz INFO:: replace_coords: 745 atoms updated. 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 109 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 110 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 111 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 ((105 "A" 1 "") (105 "A" 2 "") (105 "A" 3 "") (105 "A" 4 "") (105 "A" 5 "") (105 "A" 6 "") (105 "A" 7 "") (105 "A" 8 "") (105 "A" 9 "") (105 "A" 10 "") (105 "A" 11 "") (105 "A" 12 "") (105 "A" 13 "") (105 "A" 14 "") (105 "A" 15 "") (105 "A" 16 "") (105 "A" 17 "") (105 "A" 18 "") (105 "A" 19 "") (105 "A" 20 "") (105 "A" 21 "") (105 "A" 22 "") (105 "A" 23 "") (105 "A" 24 "") (105 "A" 25 "") (105 "A" 26 "") (105 "A" 27 "") (105 "A" 28 "") (105 "A" 29 "") (105 "A" 30 "") (105 "A" 31 "") (105 "A" 32 "") (105 "A" 33 "") (105 "A" 34 "") (105 "A" 35 "") (105 "A" 36 "") (105 "A" 37 "") (105 "A" 38 "") (105 "A" 39 "") (105 "A" 40 "") (105 "A" 41 "") (105 "A" 42 "") (105 "A" 43 "") (105 "A" 44 "") (105 "A" 45 "") (105 "A" 46 "") (105 "A" 47 "") (105 "A" 48 "") (105 "A" 49 "") (105 "A" 50 "") (105 "A" 51 "") (105 "A" 52 "") (105 "A" 53 "") (105 "A" 54 "") (105 "A" 55 "") (105 "A" 56 "") (105 "A" 57 "") (105 "A" 58 "") (105 "A" 59 "") (105 "A" 60 "") (105 "A" 61 "") (105 "A" 62 "") (105 "A" 63 "") (105 "A" 64 "") (105 "A" 65 "") (105 "A" 66 "") (105 "A" 67 "") (105 "A" 68 "") (105 "A" 69 "") (105 "A" 70 "") (105 "A" 71 "") (105 "A" 72 "") (105 "A" 73 "") (105 "A" 74 "") (105 "A" 75 "") (105 "A" 76 "") (105 "A" 77 "") (105 "A" 78 "") (105 "A" 79 "") (105 "A" 80 "") (105 "A" 81 "") (105 "A" 82 "") (105 "A" 83 "") (105 "A" 84 "") (105 "A" 85 "") (105 "A" 86 "") (105 "A" 87 "") (105 "A" 88 "") (105 "A" 89 "") (105 "A" 90 "") (105 "A" 91 "") (105 "A" 92 "") (105 "A" 93 "") (105 "B" 1 "") (105 "B" 2 "") (105 "B" 3 "") (105 "B" 4 "") (105 "B" 5 "") (105 "B" 6 "") (105 "B" 7 "") (105 "B" 8 "") (105 "B" 9 "") (105 "B" 10 "") (105 "B" 11 "") (105 "B" 12 "") (105 "B" 13 "") (105 "B" 14 "") (105 "B" 15 "") (105 "B" 16 "") (105 "B" 17 "") (105 "B" 18 "") (105 "B" 19 "") (105 "B" 20 "") (105 "B" 21 "") (105 "B" 22 "") (105 "B" 23 "") (105 "B" 24 "") (105 "B" 25 "") (105 "B" 26 "") (105 "B" 27 "") (105 "B" 28 "") (105 "B" 29 "") (105 "B" 30 "") (105 "B" 31 "") (105 "B" 32 "") (105 "B" 33 "") (105 "B" 34 "") (105 "B" 35 "") (105 "B" 36 "") (105 "B" 37 "") (105 "B" 38 "") (105 "B" 39 "") (105 "B" 40 "") (105 "B" 41 "") (105 "B" 42 "") (105 "B" 43 "") (105 "B" 44 "") (105 "B" 45 "") (105 "B" 46 "") (105 "B" 47 "") (105 "B" 48 "") (105 "B" 49 "") (105 "B" 50 "") (105 "B" 51 "") (105 "B" 52 "") (105 "B" 53 "") (105 "B" 54 "") (105 "B" 55 "") (105 "B" 56 "") (105 "B" 57 "") (105 "B" 58 "") (105 "B" 59 "") (105 "B" 60 "") (105 "B" 61 "") (105 "B" 62 "") (105 "B" 63 "") (105 "B" 64 "") (105 "B" 65 "") (105 "B" 66 "") (105 "B" 67 "") (105 "B" 68 "") (105 "B" 69 "") (105 "B" 70 "") (105 "B" 71 "") (105 "B" 72 "") (105 "B" 73 "") (105 "B" 74 "") (105 "B" 75 "") (105 "B" 76 "") (105 "B" 77 "") (105 "B" 78 "") (105 "B" 79 "") (105 "B" 80 "") (105 "B" 81 "") (105 "B" 82 "") (105 "B" 83 "") (105 "B" 84 "") (105 "B" 85 "") (105 "B" 86 "") (105 "B" 87 "") (105 "B" 88 "") (105 "B" 89 "") (105 "B" 90 "") (105 "B" 91 "") (105 "B" 92 "") (105 "B" 93 "") (105 "B" 94 "") (105 "B" 95 "") (105 "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_Thu_Jan__2_17:09:10_2020_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_Thu_Jan__2_17:09:10_2020_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_emsley_data_greg-data_insulin.res_Thu_Jan__2_17:09:10_2020_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_emsley_data_greg-data_insulin.res_Thu_Jan__2_17:09:10_2020_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 116 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 117 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 118 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 119 read successfully WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/3GP_from_dict_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz INFO:: backup file coot-backup/3GP_from_dict_Thu_Jan__2_17:09:10_2020_modification_1.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 121 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb PDB file /home/emsley/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:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb PDB file /home/emsley/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 123 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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 124 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/3GP_from_dict_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] [spec: mmdb::MinInt4 "L" 1 ""] INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 126 read successfully DEBUG:: there were 0 types with no dictionary ------------------ add_view_raw() ligand-view INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz DEBUG:: ================ refine_residue_range: 126 A 1:: 1:: :: 0 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 127 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links 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 133 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making conventional map from MTZ filename /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT INFO:: Number of observed reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.1230 seconds to read MTZ file INFO:: 0.0950 seconds to initialize map INFO:: 0.0710 seconds for FFT INFO:: 0.0090 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.1712 Map maximum: ..... 1.3430 Map minimum: ..... -0.6954 INFO:: 0.0010 seconds for contour map INFO:: 0.2990 seconds in total INFO:: making difference map from MTZ filename /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT INFO:: Number of observed reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.0730 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0660 seconds for FFT INFO:: 0.0090 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.0334 Map maximum: ..... 0.3661 Map minimum: ..... -0.1917 INFO:: 0.0000 seconds for contour map INFO:: 0.1490 seconds in total INFO:: ligand number 0 is molecule number 127 with wiggly flag: 0 in execute_ligand_search_internal() import maps from mol 134 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 DEBUG:: ================ refine_residue_range: 137 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 137 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 137.4962 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.7000 INFO:: backup file coot-backup/Fitted_ligand_#0-0_Thu_Jan__2_17:09:15_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 2.0180 and 8 are decent out of 12 DEBUG:: ================ refine_residue_range: 138 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 138 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 239.5569 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.7110 INFO:: backup file coot-backup/Fitted_ligand_#1-0_Thu_Jan__2_17:09:18_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 2.0901 and 4 are decent out of 12 DEBUG:: ================ refine_residue_range: 139 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 139 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 233.2160 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.6780 INFO:: backup file coot-backup/Fitted_ligand_#2-0_Thu_Jan__2_17:09:21_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 1.8588 and 6 are decent out of 12 DEBUG:: ================ refine_residue_range: 140 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 140 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 265.6423 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.6610 INFO:: backup file coot-backup/Fitted_ligand_#3-0_Thu_Jan__2_17:09:25_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 1.3913 and 10 are decent out of 12 DEBUG:: ================ refine_residue_range: 141 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 141 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 291.7442 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.7020 INFO:: backup file coot-backup/Fitted_ligand_#4-0_Thu_Jan__2_17:09:28_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 1.6844 and 8 are decent out of 12 DEBUG:: ================ refine_residue_range: 142 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 142 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 213.1649 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.7290 INFO:: backup file coot-backup/Fitted_ligand_#5-0_Thu_Jan__2_17:09:32_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 2.0961 and 8 are decent out of 12 DEBUG:: ================ refine_residue_range: 143 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 143 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 230.0505 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.6500 INFO:: backup file coot-backup/Fitted_ligand_#6-0_Thu_Jan__2_17:09:35_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 1.6363 and 8 are decent out of 12 DEBUG:: ================ refine_residue_range: 144 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 144 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 258.6028 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.6710 INFO:: backup file coot-backup/Fitted_ligand_#7-0_Thu_Jan__2_17:09:39_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 2.0701 and 3 are decent out of 12 DEBUG:: ================ refine_residue_range: 145 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 145 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 234.0762 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.6720 INFO:: backup file coot-backup/Fitted_ligand_#8-0_Thu_Jan__2_17:09:42_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. debug:: n_ligands_for_cluster() top_score 1.8574 and 5 are decent out of 12 DEBUG:: ================ refine_residue_range: 146 A 1:: 1:: :: 0 DEBUG:: In copy_mol_and_refine() refine range: chain :A: 1 :: 1 :: altconf "" coords mol: 146 map mol: 134 debug:: in refine_residues_vec() with altconf "" 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: 246.1442 Initial RMS Z values bonds: 4.6248 angles: 0.8127 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 Refinement elapsed time: 2.6680 INFO:: backup file coot-backup/Fitted_ligand_#9-0_Thu_Jan__2_17:09:45_2020_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 147 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 149 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 149 storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 149 INFO:: Reading coordinate file: /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb PDB file /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 150 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0230 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0160 seconds for FFT INFO:: 0.0010 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:: 0.0420 seconds in total storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 150 Sequence: ?EYTVITPGARTR Confidence: 1.0000 From : HEYTVITPGARTR Chain id: 0 Offset: 53 INFO:: backup file coot-backup/_home_emsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Thu_Jan__2_17:09:46_2020_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_Thu_Jan__2_17:09:46_2020_modification_0.pdb.gz ------------------ add_view_raw() RNA-builder-view ------- resulting_merge_info has size 2 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Matching/moving molecule number 154 to 154 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_Thu_Jan__2_17:09:46_2020_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. ------------------ add_view_raw() RNA-ghots-view INFO:: Reading coordinate file: /home/emsley/data/greg-data/1wly.pdb PDB file /home/emsley/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 155 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/1yb5.pdb PDB file /home/emsley/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: Found 1 models Model 1 had 0 links 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 156 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() returing from do_Ca_or_P_bonds_internal() with atom_centres size 0 returing from do_Ca_or_P_bonds_internal() with atom_centres size 0 INFO:: reference 155 has 750 atoms selected INFO:: moving 156 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_emsley_data_greg-data_1yb5.pdb_Thu_Jan__2_17:09:47_2020_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 returing from do_Ca_or_P_bonds_internal() with atom_centres size 0 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% ------------------ add_view_raw() SSM View WARNING:: Error reading /home/emsley/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 - Merge molecules of a ligand with a spec PASS: Merge molecules of a ligand with a spec 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 - 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 150 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" PASS: Cootaneer Beta Strand Ended 04-cootaneer.scm Running 05-rna-ghosts.scm ... Entered testcase - RNA NCS Ghosts There are 8 residues in chain "A" There are 8 residues in chain "B" PASS: RNA NCS Ghosts Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example PASS: SSM - Frank von Delft's Example Entered testcase - SSM - Alice Dawson's Example 0 "/home/emsley/data/greg-data/tutorial-modern.pdb" 2 "/home/emsley/data/greg-data/ins-code-fragment-pre.pdb" 3 "/home/emsley/data/greg-data/tutorial-modern.pdb" 4 "PTR_from_dict" 5 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 6 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 7 "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 8 "test-3hfl.map" 9 "/home/emsley/data/greg-data/tutorial-modern.pdb" 10 "mainchain-forward" 11 "/home/emsley/data/greg-data/tutorial-modern.pdb" 12 "mainchain-forwards" 13 "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 14 "atom selection from tutorial-add-terminal-1-test.pdb" 15 "/home/emsley/data/greg-data/frag-2wot.pdb" 16 "/home/emsley/data/greg-data/tutorial-modern.pdb" 17 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 18 "sphere selection from tutorial-modern.pdb" 20 "/home/emsley/data/greg-data/rotamer-test-fragment.pdb" 21 "/home/emsley/data/greg-data/eleanor-HIS.pdb" 22 "/home/emsley/data/greg-data/res098.pdb" 23 "/home/emsley/data/greg-data/tutorial-modern.pdb" 24 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 25 "/home/emsley/data/greg-data/pdb3knw.ent" 26 "/home/emsley/data/greg-data/pdb1py3.ent" 29 "/home/emsley/data/greg-data/alt-conf-pepflip-test.pdb" 30 "/home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 33 "/home/emsley/data/greg-data/tutorial-modern.pdb" 34 "atom selection from tutorial-modern.pdb" 35 "/home/emsley/data/greg-data/tutorial-modern.pdb" 36 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 37 "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 38 "/home/emsley/data/greg-data/tutorial-modern.pdb" 39 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 40 "/home/emsley/data/greg-data/tutorial-modern.pdb" 41 "/home/emsley/data/greg-data/alt-conf-waters.pdb" 42 "/home/emsley/data/greg-data/backrub-fragment.pdb" 43 "Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb" 44 "/home/emsley/data/greg-data/coords-B3A.pdb" 45 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 46 "/home/emsley/data/greg-data/test-TER-OXT.pdb" 47 "/home/emsley/data/greg-data/val.pdb" 48 "/home/emsley/data/greg-data/2yie-frag.pdb" 49 "/home/emsley/data/greg-data/4f8g.pdb" 50 "/home/emsley/data/greg-data/4f8g.pdb" 51 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 52 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 53 "/home/emsley/data/greg-data/tutorial-modern.pdb" 54 "Generic Masked Map" 55 "difference-map" 58 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 59 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 60 "averaged-map" 61 "difference-map" 62 "/home/emsley/data/greg-data/multi-carbo-coot-3.pdb" 63 "/home/emsley/data/greg-data/pdb2qc1-sans-cho.pdb" 64 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 65 "/home/emsley/data/greg-data/monomer-VAL.pdb" 66 "/home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 67 "atom selection from tutorial-modern.pdb" 68 "/home/emsley/data/greg-data/monomer-ACT.pdb" 69 "/home/emsley/data/greg-data/tutorial-modern.pdb" 70 "/home/emsley/data/greg-data/tutorial-modern.pdb" 71 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 72 "atom selection from tutorial-modern.pdb" 73 "/home/emsley/data/greg-data/tutorial-modern.pdb" 74 "/home/emsley/data/greg-data/tutorial-modern.pdb" 75 "/home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb" 76 "/home/emsley/data/greg-data/tutorial-modern.pdb" 77 "/home/emsley/data/greg-data/tutorial-modern.pdb" 78 "/home/emsley/data/greg-data/pdb3hfl.ent" 79 "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 80 "Ideal-A-form-RNA" 81 "Ideal-A-form-RNA" 82 "Ideal-A-form-DNA" 83 "Ideal-A-form-DNA" 84 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 85 "/home/emsley/data/greg-data/some-waters-with-ter.pdb" 86 "/home/emsley/data/greg-data/tm+some-waters.pdb" 87 "/home/emsley/data/greg-data/tutorial-modern.pdb" 88 "/home/emsley/data/greg-data/water-test-no-cell.pdb" 89 "/home/emsley/data/greg-data/pathological-water-test.pdb" 90 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 91 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 92 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 93 "/home/emsley/data/greg-data/tutorial-modern.pdb" 94 "/home/emsley/data/greg-data/pdb1hvv.ent" 95 "/home/emsley/data/greg-data/monomer-ACT.pdb" 96 "/home/emsley/data/greg-data/monomer-NPO.pdb" 97 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_94" 98 "/home/emsley/data/greg-data/tutorial-modern.pdb" returing from do_Ca_or_P_bonds_internal() with atom_centres size 0 INFO:: Reading coordinate file: /home/emsley/data/greg-data/2qd9.pdb PDB file /home/emsley/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 157 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/2gtn.pdb PDB file /home/emsley/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 0/337 Molecule 158 read successfully DEBUG:: there were 1 types with no dictionary INFO:: reference 157 has 169 atoms selected INFO:: moving 158 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_emsley_data_greg-data_2gtn.pdb_Thu_Jan__2_17:09:47_2020_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 159 read successfully INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0240 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0160 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:: 0.0430 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:: 1204224 out of 1204224 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0003 st.d: 0.3259 Map statistics: min: -1.4625, max: 2.4294 -1.4139 10 -1.3166 17 -1.2193 21 -1.1220 26 -1.0247 48 -0.9274 147 -0.8301 599 -0.7328 2202 -0.6355 7234 -0.5382 21636 -0.4409 54191 -0.3436 104988 -0.2463 155380 -0.1490 175625 -0.0517 165940 0.0456 135166 0.1429 101141 0.2402 76296 0.3375 58142 0.4348 43032 0.5321 31316 0.6294 22626 0.7267 15850 0.8239 11149 0.9212 7707 1.0185 5078 1.1158 3326 1.2131 2189 1.3104 1320 1.4077 786 1.5050 469 1.6023 252 1.6996 123 1.7969 69 1.8942 45 1.9915 31 2.0888 22 2.1861 16 2.2834 5 2.3807 3 2.4780 1 INFO:: installing ghost map with name :Map 160 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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 165 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_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: 165 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 165 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 165 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 165 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_5.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1t6q.ent PDB file /home/emsley/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links 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 166 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Thu_Jan__2_17:09:49_2020_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: 166 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 166 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_emsley_data_greg-data_pdb1t6q.ent_Thu_Jan__2_17:09:49_2020_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Thu_Jan__2_17:09:49_2020_modification_2.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 167 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 167 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 168 to 167 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_emsley_data_greg-data_pdb1hvv.ent_Thu_Jan__2_17:09:49_2020_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 169 to 167 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_emsley_data_greg-data_pdb1hvv.ent_Thu_Jan__2_17:09:50_2020_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 170 to 167 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_emsley_data_greg-data_pdb1hvv.ent_Thu_Jan__2_17:09:50_2020_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/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 171 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/1hvv_sigmaa.mtz INFO:: Number of observed reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO:: grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.0300 seconds to read MTZ file INFO:: 0.0200 seconds to initialize map INFO:: 0.0300 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0000 seconds for contour map INFO:: 0.0830 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 172 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 172 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 172 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 172 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 172 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 172 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 172 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 172 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 172 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 99 "atom selection from tutorial-modern.pdb" 100 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 101 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 102 "/home/emsley/data/greg-data/tutorial-modern.pdb" 103 "/home/emsley/data/greg-data/pdb1py3.ent" 104 "/home/emsley/data/greg-data/tutorial-modern.pdb" 105 "/home/emsley/data/greg-data/tutorial-modern.pdb" 106 "/home/emsley/data/greg-data/2goz-manip.pdb" 107 "/home/emsley/data/greg-data/tutorial-modern.pdb" 108 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 109 "/home/emsley/data/greg-data/HOF.RES" 110 "/home/emsley/data/greg-data/hollander.ins" 113 "/home/emsley/data/greg-data/insulin.fcf Diff-SigmaA" 114 "atom selection from insulin.res" 115 "atom selection from insulin.res" 117 "/home/emsley/data/greg-data/horma-p21.res" 118 "new-horma.ins" 119 "/home/emsley/data/greg-data/crash.hat" 120 "3GP_from_dict" 121 "/home/emsley/data/greg-data/monomer-3GP.pdb" 122 "/home/emsley/data/greg-data/test-LIG.pdb" 123 "/home/emsley/data/greg-data/test-LIG.pdb" 124 "/home/emsley/data/greg-data/tutorial-modern.pdb" 125 "3GP_from_dict" 126 "/home/emsley/data/greg-data/monomer-3GP.pdb" 127 "/home/emsley/data/greg-data/monomer-NPO.pdb" 128 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 129 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 130 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 131 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 132 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 133 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 134 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 135 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 136 "Masked (by protein)" 137 "Fitted ligand #0-0" 138 "Fitted ligand #1-0" 139 "Fitted ligand #2-0" 140 "Fitted ligand #3-0" 141 "Fitted ligand #4-0" 142 "Fitted ligand #5-0" 143 "Fitted ligand #6-0" 144 "Fitted ligand #7-0" 145 "Fitted ligand #8-0" 146 "Fitted ligand #9-0" 147 "/home/emsley/data/greg-data/monomer-3GP.pdb" 148 "Copy_of_/home/emsley/data/greg-data/monomer-3GP.pdb" 149 "/home/emsley/data/greg-data/tutorial-modern.pdb" 150 "/home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb" 151 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 152 "Ideal-A-form-RNA" 155 "/home/emsley/data/greg-data/1wly.pdb" 156 "/home/emsley/data/greg-data/1yb5.pdb" PASS: SSM - Alice Dawson's Example Entered testcase - SSM by atom selection [JED Example] PASS: SSM by atom selection [JED Example] Ended 06-ssm.scm Running 07-ncs.scm ... Entered testcase - NCS maps test PASS: NCS maps test Entered testcase - NCS chains info NCS info: (("A" "B")) PASS: NCS chains info Entered testcase - NCS deviation info PASS: NCS deviation info Entered testcase - NCS Residue Range copy PASS: NCS Residue Range copy Entered testcase - NCS Residue Range edit to all chains result: (#t #t) PASS: NCS Residue Range edit to all chains Entered testcase - Manual NCS ghosts generates correct NCS chain ids NCS ghost chain IDs pre: (("B" "A" "C" "D")) NCS ghost chain IDs post: (("B" "A" "C" "D")) PASS: Manual NCS ghosts generates correct NCS chain ids Entered testcase - NCS maps overwrite existing maps ==== test-name: "Map 172 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 172 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 172 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 runerror (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 INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 181 read successfully DEBUG:: there were 0 types with no dictionary Entering test: OXT in restraints? INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/ There are 153 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/n/NA.cif There are 2 data in /home/emsley/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.1414 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/emsley/ccp4/ccp4-7.0/lib/data/monomers/ There are 153 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/n/NA.cif INFO:: Reading coordinate file: /home/emsley/data/greg-data/hideous-OXT.pdb PDB file /home/emsley/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom created 8 bond restraints created 10 angle restraints created 2 plane restraints created 1 chiral vol restraints created 3 torsion restraints created 28 restraints INFO:: make_restraints(): made 13 non-bonded restraints initial distortion_score: 4671.5846 Initial RMS Z values bonds: 5.4612 angles: 16.4829 torsions: 0.3071 planes: 19.5074 non-bonded: 0.0000 chiral vol: 1.0066 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 379) at 7.7980 Final Estimated RMS Z Scores: bonds: 0.1934 angles: 0.7875 torsions: 0.0791 planes: 0.0047 non-bonded: 0.0000 chiral vol: 0.0006 rama plot: N/A start_pos: N/A GemanMcCl: N/A refinement_took 0.0070 seconds OXT out of plane distance: 0.0003 OXT->O distance: 2.1787 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/emsley/data/greg-data/frag-2wot.pdb PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 bad residues for phi,psi calculation bad residues for phi,psi calculation PASS: Residues for phi,psi are close enough to be considered linked ning a Python function test_val_2 passed test_val_3 passed PASS: Test running a Python function Entered testcase - Internal/External Molecule Numbers match PASS: Internal/External Molecule Numbers match Entered testcase - spacegroup operators to space group conversion PASS: spacegroup operators to space group conversion Ended 08-utils.scm Running 09-internal.scm ... Entered testcase - Test internal functions PASS: Test internal functions Ended 09-internal.scm === greg-tests Summary === # of testcases attempted 130 # of expected passes 130 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # 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 130 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 ObjectCache: Leaked 0004 refs to

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

ObjectCache: Leaked 0004 refs to test_coot: coot test passed