testing with greg testing with greg currently we are here: /home/paule/autobuild/building/emsley-vm-debian-7-7_2019-04-01__T10_36_02/coot-0.8.9.2-pre Mon 1 Apr 12:12:11 BST 2019 WARNING:: ccp4 setup file setup-ccp4 does not exist. /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/ INFO:: Reading coordinate file: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) INFO:: coot.py imported Running python script /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Afternoon Paul, Welcome to Coot version 0.8.9.2-pre (set-display-intro-string "Good Afternoon Paul, Welcome to Coot version 0.8.9.2-pre") (use-graphics-interface-state) (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good afternoon root. Welcome to Coot 0.8.9.2-pre") (set-display-lists-for-maps 0) load /home/paule/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 0) (unset-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 12.60) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run command-line-greg.scm INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary Molecule number -5 is not a valid model molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/2WF6.cif mmCIF file /home/paule/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 1 read successfully DEBUG:: there were 3 types with no dictionary in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Reading coordinate file: /home/paule/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/paule/data/greg-data/ins-code-fragment-pre.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 2 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Creating directory coot-backup INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_Apr__1_12:12:43_2019_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_Apr__1_12:12:43_2019_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_Apr__1_12:12:43_2019_modification_2.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 3 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_0.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_1.pdb.gz INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_2.pdb.gz INFO:: Matching/moving molecule number 4 to 3 INFO:: LSQ matched 15 atoms INFO:: 15 matched atoms had: mean devi: 0.605779 rms devi: 0.634415 max devi: 0.938213 min devi: 0.391381 INFO:: Axis orientation: ( -0.5848, -0.7505, 0.3079) INFO:: Rotation in CCP4 Polar Angles: Polar = (72.0654,-127.924,156.99) INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_3.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.2638, 0.7224, -0.6392| | 0.9632, 0.1612, -0.2152| | -0.05243, -0.6724, -0.7383| ( 69.15, -27.17, 32.75) No unit cell for this molecule, hence no fractional matrix. INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_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 ------ after matching, check the torsions torsion check: ( N CA CB CG ) was -60.01 should be -47.18 and is -47.18 torsion check: ( CA CB CG CD2) was -90.31 should be -56.84 and is -56.84 INFO:: rotated 2 torsions in matching torsions INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:12:43_2019_modification_0.pdb.gz ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] [spec: 1 "A" 101 ""] INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:12:43_2019_modification_1.pdb.gz INFO:: created 40 restraints created 16 bond restraints created 22 angle restraints created 1 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 610 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 55734.43 Initial RMS Z values bonds: 8.93 angles: 9.45 torsions: N/A planes: 12.49 non-bonded: 83.62 chiral vol: 0.26 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 61) at 60.39 Final Estimated RMS Z Scores: bonds: 0.42 angles: 1.33 torsions: N/A planes: 0.57 non-bonded: 0.00 chiral vol: 2.27 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 0.00 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:12:43_2019_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/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.50 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 22.18 seconds to read MTZ file INFO:: 0.01 seconds to initialize map INFO:: 2.15 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 2.98 Map minimum: ..... -0.88 INFO:: 0.00 seconds for contour map INFO:: 24.34 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT INFO:: Number of observed reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.50 INFO:: grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.03 seconds to read MTZ file INFO:: 0.00 seconds to initialize map INFO:: 0.02 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.31 Map maximum: ..... 2.98 Map minimum: ..... -0.88 INFO:: 0.00 seconds for contour map INFO:: 0.05 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz INFO:: Number of observed reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.50 INFO:: grid sampling...Nuvw = ( 64, 96, 90) INFO:: 8.25 seconds to read MTZ file INFO:: 0.08 seconds to initialize map INFO:: 0.02 seconds for FFT INFO:: 0.00 seconds for statistics Map mean: ........ 0.00 Map sigma: ....... 0.26 Map maximum: ..... 1.72 Map minimum: ..... -1.03 INFO:: 0.00 seconds for contour map INFO:: 8.35 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: 1.72 -1.00 1 -0.93 8 -0.86 23 -0.79 96 -0.72 305 -0.66 714 -0.59 1587 -0.52 2927 -0.45 5202 -0.38 7937 -0.31 11655 -0.24 16895 -0.17 24542 -0.11 34962 -0.04 43098 0.03 41219 0.10 29087 0.17 15906 0.24 8720 0.31 6095 0.38 4870 0.45 4308 0.51 3717 0.58 3304 0.65 2688 0.72 2065 0.79 1620 0.86 1097 0.93 786 1.00 479 1.06 257 1.13 146 1.20 73 1.27 35 1.34 20 1.41 14 1.48 11 1.55 7 1.61 3 1.68 1 1.75 0 INFO:: n grid points: 276480 INFO:: mean before filtering: 0.00 INFO:: variance before filtering: 0.07 INFO:: filter by ignoring 210 of 276480 counts ( = 0.0760%) with values around -0.0054 from bin 3737 of 10000 Map mean: ........ 0.0000 Map rmsd: ........ 0.2605 Map maximum: ..... 1.7179 Map minimum: ..... -1.0339 WARNING:: Error reading . . is a directory. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 9 read successfully DEBUG:: there were 0 types with no dictionary /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. ERROR 42 READ: Duplicate sequence number and insertion code. LINE #868 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb INFO:: 8375 fragments found in total of which 0 were 5 peptides not backwards A contains 94 residues from 1 to 93 target fragment start res: 10 had 29 db fragment hits, ilength=6 target fragment start res: 13 had 1772 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 16 merge fragments 10 to 20 with 2 fit sets to merge The merging is complete mainchain_fragment from 10 to 20 done mainchain_fragment successfully set cell and symmetry INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 11 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:08_2019_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:4654): Gtk-CRITICAL **: IA__gtk_widget_show: assertion `GTK_IS_WIDGET (widget)' failed INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 13 read successfully DEBUG:: there were 0 types with no dictionary fitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 1 offset: -1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:09_2019_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:09_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 15 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 16 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0520 seconds in total fitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:09_2019_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:09_2019_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:09_2019_modification_2.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/rotamer-test-fragment.pdb PDB file /home/paule/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 20 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] WARNING:: Error reading /home/paule/data/greg-data/eleanor-HIS.pdb INFO:: Reading coordinate file: /home/paule/data/greg-data/res098.pdb PDB file /home/paule/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 21 read successfully DEBUG:: there were 0 types with no dictionary INFO:: created 19 restraints created 10 bond restraints created 8 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 7 angle links 5 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 129 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 599.3325 Initial RMS Z values bonds: 0.1989 angles: 0.4071 torsions: N/A planes: 0.5035 non-bonded: 4.4321 chiral vol: 0.1627 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 239) at 9.9937 Final Estimated RMS Z Scores: bonds: 0.0729 angles: 0.6197 torsions: N/A planes: 0.5967 non-bonded: 0.0000 chiral vol: 0.5924 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 146.2020 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Mon_Apr__1_12:15:10_2019_modification_0.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0000 seconds for contour map INFO:: 0.0510 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:10_2019_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_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:10_2019_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.7495 Good afternoon root. Welcome to Coot 0.8.9.2-pre. === greg-tests tests === Loading greg-tests/begin.grg ... =============================================================== ==================== Testing ================================== =============================================================== Loaded greg-tests/begin.grg Running 01-pdb+mtz.scm ... Entered testcase - Post Go To Atom no molecules PASS: Post Go To Atom no molecules Entered testcase - Close bad molecule PASS: Close bad molecule Entered testcase - Read coordinates test PASS: Read coordinates test Entered testcase - New molecule from bogus molecule PASS: New molecule from bogus molecule Entered testcase - Don't crash on empty NCS from mmCIF file closing molecule number 1 PASS: Don't crash on empty NCS from mmCIF file Entered testcase - New molecule from bogus atom selection INFO:: pre-n-molecules 2 post-n-molecules 2 PASS: New molecule from bogus atom selection Entered testcase - ins code change and Goto atom over an ins code break pre and post ins codes: "" "A" pass: ("A" 68 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "A" " CA ") pass: ("A" 68 "" " CA ") pass: ("A" 66 "" " CA ") PASS: ins code change and Goto atom over an ins code break Entered testcase - Replace Residue gets correct residue number 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: 1.33591012485164 PASS: Replace Residue gets correct residue number Entered testcase - Read a bogus map PASS: Read a bogus map Entered testcase - Read MTZ test PASS: Read MTZ test Entered testcase - Auto-read bad MTZ test got status: #() got status: #() PASS: Auto-read bad MTZ test Entered testcase - Map Sigma INFO:: map sigmas 0.311501026153564 #f PASS: Map Sigma Entered testcase - Another Level Test PASS: Another Level Test Entered testcase - Sharpen map from map PASS: Sharpen map from map Entered testcase - db-main makes mainchain PASS: db-main makes mainchain Entered testcase - Negative Residues in db-mainchain don't cause a crash PASS: Negative Residues in db-mainchain don't cause a crash Entered testcase - Set Atom Attribute Test PASS: Set Atom Attribute Test Entered testcase - Add Terminal Residue Test PASS: Add Terminal Residue Test Entered testcase - Adding residue by phi psi, no crash PASS: Adding residue by phi psi, no crash Entered testcase - Add Terminal Residue O Position Add terminal residue bond check dd-1: 0.14997610541894 Add terminal residue bond check dd-2: 2.25586252670689 PASS: Add Terminal Residue O Position Entered testcase - Select by Sphere Sphere mol: there are 4 residues in chain "B" Found 20 sphere atoms PASS: Select by Sphere Entered testcase - Test Views PASS: Test Views Entered testcase - Label Atoms and Delete PASS: Label Atoms and Delete Entered testcase - Rotamer outliers PASS: Rotamer outliers Entered testcase - HIS with unusual atom order rotates correct fragment for 180 sidechain flip BAD imol for 180 sidechain flip test imol: -1 FAIL: HIS with unusual atom order rotates correct fragment for 180 sidechain flip Entered testcase - Alt Conf Occ Sum Reset For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 PASS: Alt Conf Occ Sum Reset Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue PASS: Correct occupancies after auto-fitINFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3knw.ent PDB file /home/paule/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 185/199 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 24 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3knw.ent_Mon_Apr__1_12:15:10_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 25 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1py3.ent_Mon_Apr__1_12:15:11_2019_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 rotamer on alt-confed residue Entered testcase - Rotamers work on MSE se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746)) se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616)) PASS: Rotamers work on MSE Entered testcase - Hs are correctly swapped on a TYR bond-length-within-tolerance? bond-length 0.93069991132425 with target 0.93 and tolerance 0.02 for atom ((" CD1" "") (1.0 (22.3700008392334 0.288300007581711 0.351099997758865 0.210400000214577 0.0551000013947487 0.0124000003561378 0.00350000010803342) " C" "") (61.2610015869141 -13.2200002670288 1.25)) is ((" HD1" "") (1.0 22.7800006866455 " H" "") (61.4099998474121 -12.8690004348755 2.09899997711182)) bond-length-within-tolerance? bond-length 0.930136198469449 with target 0.93 and tolerance 0.02 for atom ((" CD2" "") (1.0 (24.4099998474121 0.258899986743927 0.405699998140335 0.262800008058548 0.0627999976277351 -0.0269000008702278 -0.00970000028610229) " C" "") (59.9500007629395 -13.3459997177124 -0.740000009536743)) is ((" HD2" "") (1.0 24.3099994659424 " H" "") (59.2050018310547 -13.0869998931885 -1.23300004005432)) bond-length-within-tolerance? bond-length 0.930888837109095 with target 0.93 and tolerance 0.02 for atom ((" CE1" "") (1.0 (22.1599998474121 0.280600011348724 0.314999997615814 0.246199995279312 0.0603000000119209 -0.0186000000685453 -0.0172000005841255) " C" "") (62.1650009155273 -14.1079998016357 0.726000010967255)) is ((" HE1" "") (1.0 22.1200008392334 " H" "") (62.9140014648438 -14.3520002365112 1.22200000286102)) bond-length-within-tolerance? bond-length 0.929591631283786 with target 0.93 and tolerance 0.02 for atom ((" CE2" "") (1.0 (23.9099998474121 0.281399995088577 0.359200000762939 0.267500013113022 0.0529999993741512 -0.0285000000149012 -0.0131999999284744) " C" "") (60.8559989929199 -14.2670001983643 -1.29900002479553)) is ((" HE2" "") (1.0 23.5400009155273 " H" "") (60.7249984741211 -14.6049995422363 -2.15499997138977)) INFO:: 25 residues had their atoms swapped INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 26 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0520 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/paule/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 28 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-pepflip-test.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 29 read successfully DEBUG:: there were 0 types with no dictionary omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_2.pdb.gz INFO:: created 21 restraints created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 1 bond links 4 angle links 3 plane links 1 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 7 angle links 5 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 138 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 4781.3414 Initial RMS Z values bonds: 15.4585 angles: 7.1242 torsions: N/A planes: 1.8999 non-bonded: 29.0131 chiral vol: 3.0446 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 38) at -4775.0334 Final Estimated RMS Z Scores: bonds: 0.9643 angles: 0.7789 torsions: N/A planes: 2.3214 non-bonded: 0.0431 chiral vol: 0.1157 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 147.1530 Refinement elapsed time: 0.0130 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.4516 INFO:: created 32 restraints created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints Link restraints: 1 bond links 4 angle links 3 plane links 1 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 7 angle links 5 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 222 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -5899.3677 Initial RMS Z values bonds: 0.9474 angles: 1.6100 torsions: N/A planes: 2.8722 non-bonded: 0.1736 chiral vol: 0.4224 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 3) at -6027.2788 Final Estimated RMS Z Scores: bonds: 0.9354 angles: 0.6993 torsions: N/A planes: 2.3820 non-bonded: 0.0289 chiral vol: 0.1238 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 147.2330 Refinement elapsed time: 0.0120 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 30 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz cliquize 12 spinables for altconf --------------------------- 12 cliques ---------------- omega: 1 -177.7480 degrees INFO This is a TRANS peptide - making it CIS INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 32 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_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_Mon_Apr__1_12:15:11_2019_modification_1.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 34 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0280 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0510 seconds in total INFO:: created 11 restraints created 6 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 80 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -3168.4874 Initial RMS Z values bonds: 2.0711 angles: 1.0696 torsions: N/A planes: 0.6113 non-bonded: 3.4160 chiral vol: 1.4620 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 64) at -3413.0046 Final Estimated RMS Z Scores: bonds: 1.1108 angles: 1.5126 torsions: N/A planes: 0.2626 non-bonded: 0.3751 chiral vol: 1.2342 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 147.4210 Refinement elapsed time: 0.0060 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 36 read successfully DEBUG:: there were 0 types with no dictionary DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: created 81 restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints 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: -15654.1423 Initial RMS Z values bonds: 1.7426 angles: 1.2676 torsions: N/A planes: 0.8383 non-bonded: 0.0007 chiral vol: 0.8944 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 27) at -16041.7470 Final Estimated RMS Z Scores: bonds: 1.0091 angles: 0.6518 torsions: N/A planes: 0.5835 non-bonded: 0.0000 chiral vol: 0.2404 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 147.5380 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:11_2019_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. 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: -7143.5789 Initial RMS Z values bonds: 0.9807 angles: 1.0175 torsions: N/A planes: 1.7875 non-bonded: 5.2955 chiral vol: 10.2816 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 58) at -15651.6817 Final Estimated RMS Z Scores: bonds: 1.9471 angles: 1.7856 torsions: N/A planes: 1.6126 non-bonded: 0.0500 chiral vol: 1.7692 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 147.6490 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:11_2019_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 37 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0510 seconds in total INFO:: 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: -3041.7182 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -11414.3979 Final Estimated RMS Z Scores: bonds: 2.0037 angles: 1.9678 torsions: N/A planes: 1.7242 non-bonded: 0.0604 chiral vol: 2.0928 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 147.8120 Refinement elapsed time: 0.0630 ---------------------------------------------- ---------------------------------------------- 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: 4868.0924 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 75) at -2825.8990 Final Estimated RMS Z Scores: bonds: 0.8192 angles: 1.3983 torsions: N/A planes: 1.8356 non-bonded: 0.0188 chiral vol: 1.2862 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 147.9010 Refinement elapsed time: 0.0890 ---------------------------------------------- ---------------------------------------------- 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: 6111.3710 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 73) at -1514.1070 Final Estimated RMS Z Scores: bonds: 0.6156 angles: 1.2624 torsions: N/A planes: 1.8069 non-bonded: 0.0116 chiral vol: 1.0780 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 148.0140 Refinement elapsed time: 0.1120 ---------------------------------------------- ---------------------------------------------- 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: 6580.0776 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 5) at -1026.8395 Final Estimated RMS Z Scores: bonds: 0.5241 angles: 1.1747 torsions: N/A planes: 1.7905 non-bonded: 0.0085 chiral vol: 0.9902 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 148.2010 Refinement elapsed time: 0.1870 ---------------------------------------------- ---------------------------------------------- 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: 6807.3837 Initial RMS Z values bonds: 0.9358 angles: 1.0580 torsions: N/A planes: 1.9846 non-bonded: 7.4770 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 58) at -793.2879 Final Estimated RMS Z Scores: bonds: 0.4709 angles: 1.1159 torsions: N/A planes: 1.7831 non-bonded: 0.0070 chiral vol: 0.9340 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 148.4380 Refinement elapsed time: 0.2360 INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 39 read successfully DEBUG:: there were 0 types with no dictionary ---------------------------------------------- ---------------------------------------------- ERROR:: A: last_restraints no cleared up ---------------------------------------------- ---------------------------------------------- INFO:: created 52 restraints created 23 bond restraints created 25 angle restraints created 0 plane restraints created 4 chiral vol restraints 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: -1086.3897 Initial RMS Z values bonds: 1.6203 angles: 1.0091 torsions: N/A planes: 0.7374 non-bonded: 0.0256 chiral vol: 0.5795 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 35) at -1239.1218 Final Estimated RMS Z Scores: bonds: 0.1620 angles: 0.5206 torsions: N/A planes: 0.3319 non-bonded: 0.0023 chiral vol: 0.2772 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 148.5080 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:12_2019_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=0.170920995733268 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.28254206006481 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 2.004" 2.00372433662415) ("Angles" "Angles: 1.968" 1.96783602237701) ("Planes" "Planes: 1.724" 1.72420871257782) ("Non-bonded" "Non-bonded: 0.246" 0.245682418346405) ("Chirals" "Chirals: 2.093" 2.09279537200928))) ow factor: 1.94714111089706 INFO:: setting refinement weight to 15.825462010273 refinement results: ("" 0 (("Bonds" "Bonds: 0.819" 0.819224894046783) ("Angles" "Angles: 1.398" 1.39832580089569) ("Planes" "Planes: 1.836" 1.83556282520294) ("Non-bonded" "Non-bonded: 0.137" 0.137185722589493) ("Chirals" "Chirals: 1.286" 1.28615963459015))) ow factor: 1.33481828868389 INFO:: setting refinement weight to 8.88202742880352 refinement results: ("" 0 (("Bonds" "Bonds: 0.616" 0.615578889846802) ("Angles" "Angles: 1.262" 1.26242864131927) ("Planes" "Planes: 1.807" 1.8069269657135) ("Non-bonded" "Non-bonded: 0.108" 0.107924073934555) ("Chirals" "Chirals: 1.078" 1.07801687717438))) ow factor: 1.19073784351349 INFO:: setting refinement weight to 6.26440470144893 refinement results: ("" 0 (("Bonds" "Bonds: 0.524" 0.524065494537354) ("Angles" "Angles: 1.175" 1.17469692230225) ("Planes" "Planes: 1.791" 1.79053711891174) ("Non-bonded" "Non-bonded: 0.092" 0.0923675745725632) ("Chirals" "Chirals: 0.990" 0.990249395370483))) ow factor: 1.11988723278046 INFO:: setting refinement weight to 4.99495091490859 refinement results: ("" 0 (("Bonds" "Bonds: 0.471" 0.470898509025574) ("Angles" "Angles: 1.116" 1.1158994436264) ("Planes" "Planes: 1.783" 1.78314650058746) ("Non-bonded" "Non-bonded: 0.084" 0.0838774889707565) ("Chirals" "Chirals: 0.934" 0.93397319316864))) ow factor: 1.07597941160202 PASS: Refinement gives useful results Entered testcase - Neighbour-Refine doesn't destroy disulfide bonds bond-length-within-tolerance? bond-length 2.03286102466317 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.5975971221924 27.5079345703125 11.2516946792603)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7325477600098 27.0097732543945 9.48080539703369)) 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: -1239.1218 Initial RMS Z values bonds: 0.1620 angles: 0.5206 torsions: N/A planes: 0.3319 non-bonded: 0.0023 chiral vol: 0.2772 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -1239.1230 Final Estimated RMS Z Scores: bonds: 0.1610 angles: 0.5205 torsions: N/A planes: 0.3321 non-bonded: 0.0023 chiral vol: 0.2790 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 148.5330 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:12_2019_modification_1.pdb.gz INFO:: replace_coords: 27 atoms updated. bond-length-within-tolerance? bond-length 2.03298326695991 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.597599029541 27.5079555511475 11.2517795562744)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7326126098633 27.0097522735596 9.48073101043701)) INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-waters.pdb PDB file /home/paule/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 40 read successfully DEBUG:: there were 0 types with no dictionary masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-waters.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: Reading coordinate file: /home/paule/data/greg-data/backrub-fragment.pdb PDB file /home/paule/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 41 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Mon_Apr__1_12:15:13_2019_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/coords-B3A.pdb PDB file /home/paule/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 43 read successfully DEBUG:: there were 1 types with no dictionary INFO:: created 11 restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 5 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2.9511 Initial RMS Z values bonds: 0.6619 angles: 0.3737 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.2500 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 23) at 0.0000 Final Estimated RMS Z Scores: bonds: 0.0014 angles: 0.0027 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0012 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 148.8480 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/lib-B3A.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/lib-B3A.cif had no bond restraints INFO:: created 11 restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 5 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 0.0000 Initial RMS Z values bonds: 0.0014 angles: 0.0027 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0012 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at 0.0000 Final Estimated RMS Z Scores: bonds: 0.0003 angles: 0.0026 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0007 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 148.9580 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_Apr__1_12:15:13_2019_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. Welcome to Coot INFO:: created 11 restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 5 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 3.0185 Initial RMS Z values bonds: 0.6708 angles: 0.3753 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.2536 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 16) at 0.0000 Final Estimated RMS Z Scores: bonds: 0.0004 angles: 0.0004 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.0002 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 149.0760 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_Apr__1_12:15:13_2019_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: making map from mtz filename /home/paule/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:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0510 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. INFO:: Reading coordinate file: /home/paule/data/greg-data/test-TER-OXT.pdb PDB file /home/paule/data/greg-data/test-TER-OXT.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 45 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_test-TER-OXT.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.0897,14.9163) B-factor: 45.0000 debug:: add_OXT_to_residue() returns istat 1 WARNING:: This residue already has an OXT - aborting debug:: add_OXT_to_residue() returns istat 0 INFO:: Reading coordinate file: /home/paule/data/greg-data/val.pdb PDB file /home/paule/data/greg-data/val.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 46 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_home_paule_data_greg-data_val.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/2yie-frag.pdb PDB file /home/paule/data/greg-data/2yie-frag.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 47 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_2yie-frag.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0404 rms devi: 0.0472 max devi: 0.0833 min devi: 0.0130 INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 48 read successfully DEBUG:: there were 1 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0435 rms devi: 0.0478 max devi: 0.0740 min devi: 0.0148 INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 49 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0394 rms devi: 0.0445 max devi: 0.0695 min devi: 0.0151 INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0300 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0000 seconds for contour map INFO:: 0.0520 seconds in total INFO:: making map from mtz filename /home/paule/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:: 0.0280 seconds to read MTZ file INFO:: 0.0330 seconds to initialize map INFO:: 0.0390 seconds for FFT INFO:: 0.0060 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0518 Map minimum: ..... -0.9217 INFO:: 0.0010 seconds for contour map INFO:: 0.1070 seconds in total INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 52 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.0014 st.d: 0.3056 Map statistics: min: -0.8750, max: 2.9776 -0.8269 9 -0.7306 46 -0.6343 403 -0.5379 2065 -0.4416 7564 -0.3453 17348 -0.2490 26177 -0.1527 33633 -0.0564 40439 0.0400 41126 0.1363 21610 0.2326 10119 0.3289 5756 0.4252 4384 0.5215 3595 0.6178 3168 0.7142 2681 0.8105 2161 0.9068 1759 1.0031 1314 1.0994 958 1.1957 645 1.2921 455 1.3884 271 1.4847 175 1.5810 108 1.6773 59 1.7736 34 1.8699 17 1.9663 7 2.0626 2 2.1589 1 2.2552 4 2.3515 1 2.4478 0 2.5442 1 2.6405 0 2.7368 0 2.8331 0 2.9294 0 3.0257 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: (0.923012793064117 0.928160607814789 0.963148593902588 0.588746011257172 0.692066550254822 0.751977026462555 0.68085777759552 0.954908907413483 1.00084149837494 0.981854736804962 0.726146459579468) 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: 0.0601 Map statistics: min: -2.7883, max: 0.7305 -2.7443 1 -2.6564 1 -2.5684 1 -2.4804 1 -2.3925 1 -2.3045 1 -2.2165 0 -2.1285 1 -2.0406 0 -1.9526 3 -1.8646 1 -1.7767 1 -1.6887 5 -1.6007 3 -1.5128 4 -1.4248 6 -1.3368 21 -1.2488 16 -1.1609 41 -1.0729 35 -0.9849 54 -0.8970 68 -0.8090 85 -0.7210 108 -0.6331 116 -0.5451 145 -0.4571 148 -0.3692 181 -0.2812 209 -0.1932 264 -0.1052 356 -0.0173 223669 0.0707 639 0.1587 658 0.2466 505 0.3346 414 0.4226 223 0.5105 85 0.5985 22 0.6865 4 0.7744 0 diff-high-values: (0.00255919783376157 0.0010033113649115 0.00106657086871564 -0.00237772101536393 0.00169637822546065 7.11891916580498e-4 0.00212934077717364 0.00194923370145261 0.00229484355077147 6.56086718663573e-4 0.00835348293185234) diff-low-values: (-0.887997210025787 -0.79390150308609 -1.18933153152466 -1.06666219234467 -0.988452911376953 -0.759092628955841 -0.748683929443359 -0.650666356086731 -0.90451979637146 -0.545242130756378) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 55 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0280 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0000 seconds for contour map INFO:: 0.0510 seconds in total INFO:: making map from mtz filename /home/paule/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:: 0.0280 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0510 seconds in total INFO:: making map from mtz filename /home/paule/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:: 0.0280 seconds to read MTZ file INFO:: 0.0450 seconds to initialize map INFO:: 0.0510 seconds for FFT INFO:: 0.0090 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 3.0713 Map minimum: ..... -0.8775 INFO:: 0.0020 seconds for contour map INFO:: 0.1350 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 108, 132, 64) 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: -0.8734, max: 2.9750 -0.8253 9 -0.7291 49 -0.6328 422 -0.5366 2147 -0.4404 7837 -0.3442 17839 -0.2480 26781 -0.1518 34418 -0.0556 41152 0.0406 36651 0.1368 21808 0.2330 10320 0.3293 5945 0.4255 4553 0.5217 3766 0.6179 3294 0.7141 2796 0.8103 2261 0.9065 1818 1.0027 1374 1.0989 984 1.1951 684 1.2914 472 1.3876 284 1.4838 182 1.5800 106 1.6762 63 1.7724 39 1.8686 15 1.9648 10 2.0610 2 2.1572 2 2.2535 5 2.3497 2 2.4459 1 2.5421 2 2.6383 1 2.7345 0 2.8307 1 2.9269 0 3.0231 1 Map statistics: mean: 0.0000 st.d: 0.0011 Map statistics: min: -0.0069, max: 0.0119 -0.0066 5 -0.0062 21 -0.0057 31 -0.0052 53 -0.0047 114 -0.0043 221 -0.0038 460 -0.0033 817 -0.0029 1522 -0.0024 2764 -0.0019 4797 -0.0015 9242 -0.0010 19273 -0.0005 40373 -0.0000 61229 0.0004 44297 0.0009 20929 0.0014 9475 0.0018 4785 0.0023 2778 0.0028 1678 0.0032 1172 0.0037 689 0.0042 491 0.0046 288 0.0051 198 0.0056 151 0.0061 102 0.0065 56 0.0070 37 0.0075 18 0.0079 10 0.0084 10 0.0089 3 0.0093 1 0.0098 3 0.0103 2 0.0108 0 0.0112 0 0.0117 0 0.0122 1 INFO:: Reading coordinate file: /home/paule/data/greg-data/multi-carbo-coot-3.pdb PDB file /home/paule/data/greg-data/multi-carbo-coot-3.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 61 read successfully DEBUG:: there were 2 types with no dictionary INFO:: created 138 restraints created 46 bond restraints created 82 angle restraints created 2 plane restraints created 8 chiral vol restraints DEBUG:: find_link_type_complicado() find_glycosidic_linkage_type() returns "ALPHA1-4" Link restraints: 1 bond links 3 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 799 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2651.7158 Initial RMS Z values bonds: 6.1616 angles: 2.8528 torsions: N/A planes: 0.0835 non-bonded: 0.2115 chiral vol: 0.9035 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 887) at 15.9904 Final Estimated RMS Z Scores: bonds: 0.1009 angles: 0.4225 torsions: N/A planes: 0.0264 non-bonded: 0.0002 chiral vol: 0.1561 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 150.8740 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-3.pdb_Mon_Apr__1_12:15:15_2019_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 0.311072021722794 and diff-map: 0.00106883328408003 PASS: Simple Averaged maps Entered testcase - Make a glycosidic linkage bond-length: 2.2472998823295: bond-length: 1.44437928674295: bond-length-within-tolerance? bond-length 1.44437928674295 with target 1.439 and tolerance 0.04 for atom ((" O4 " "") (1.0 20.0 " O" "") (-3.95734977722168 20.753511428833 1.51749432086945)) is ((" C1 " "") (1.0 20.0 " C" "") (-3.19250345230103 21.6129570007324 2.39076113700867)) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb PDB file /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 3 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 1/110 Molecule 62 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0520 seconds in total ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-VAL.pdb PDB file /home/paule/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 64 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 1 CB INFO:: created 40 restraints created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 44 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 4.9970 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.4516 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.2482 Final Estimated RMS Z Scores: bonds: 0.0122 angles: 0.0949 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.1454 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 195.9980 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 64 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 INFO:: created 40 restraints created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 44 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 4.9970 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.4516 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.2482 Final Estimated RMS Z Scores: bonds: 0.0122 angles: 0.0949 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.1454 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 196.0670 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. PASS: Make a glycosidic linkage Entered testcase - Refine an NAG-ASN Link Exception: (missing-atom-1) UNRESOLVED: Refine an NAG-ASN Link Entered testcase - Test for flying hydrogens on undo bond-length-within-tolerance? bond-length 0.960061691781605 with target 0.96 and tolerance 0.02 for atom (("HG11" "") (1.0 20.0 " H" "") (3.4704897403717 -0.190908700227737 -1.96913886070251)) is ((" CG1" "") (1.0 20.0 " C" "") (2.87013721466064 -0.207151547074318 -1.22011852264404)) INFO:: Reading coordinate file: /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 65 read successfully DEBUG:: there were 0 types with no dictionary INFO:: created 49 restraints created 17 bond restraints created 31 angle restraints created 0 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 67 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 903.0633 Initial RMS Z values bonds: 5.6211 angles: 3.4330 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.7534 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 165) at 0.4747 Final Estimated RMS Z Scores: bonds: 0.0094 angles: 0.1210 torsions: N/A planes: N/A non-bonded: 0.0000 chiral vol: 0.1385 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 196.1170 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Mon_Apr__1_12:16:00_2019_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 0.959993508181978 with target 0.96 and tolerance 0.02 for atom (("HD11" "") (1.0 10.5299997329712 " H" "") (-10.1156616210938 6.52059507369995 7.01407289505005)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977)) bond-length-within-tolerance? bond-length 0.96002780270247 with target 0.96 and tolerance 0.02 for atom (("HD12" "") (1.0 10.1300001144409 " H" "") (-9.7598762512207 5.68341684341431 5.73144054412842)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977)) bond-length-within-tolerance? bond-length 0.959946651623676 with target 0.96 and tolerance 0.02 for atom (("HD13" "") (1.0 10.5600004196167 " H" "") (-11.027907371521 5.31390428543091 6.58492517471313)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977)) bond-length-within-tolerance? bond-length 0.959995371308682 with target 0.96 and tolerance 0.02 for atom (("HD21" "") (1.0 10.1499996185303 " H" "") (-7.9939432144165 3.15288591384888 7.14437961578369)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627)) bond-length-within-tolerance? bond-length 0.960016201142166 with target 0.96 and tolerance 0.02 for atom (("HD22" "") (1.0 10.3000001907349 " H" "") (-9.20783233642578 3.14652538299561 6.14453363418579)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627)) bond-length-within-tolerance? bond-length 0.959897847605806 with target 0.96 and tolerance 0.02 for atom (("HD23" "") (1.0 10.6499996185303 " H" "") (-8.02846336364746 4.16698122024536 5.94336414337158)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627)) INFO:: created 28 restraints created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 40 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 2873.4804 Initial RMS Z values bonds: 1.1515 angles: 0.8476 torsions: N/A planes: 3.0558 non-bonded: 79.8585 chiral vol: 0.7578 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 50) at -324.3456 Final Estimated RMS Z Scores: bonds: 0.2820 angles: 0.2076 torsions: N/A planes: 0.1840 non-bonded: 0.0090 chiral vol: 0.0522 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 196.1730 Refinement elapsed time: 0.0120 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_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: 2.62799378529819: bond-length-within-tolerance? bond-length 2.62799378529819 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.2963485717773 4.44178247451782 19.7638034820557)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.524772644043 6.66353750228882 19.08473777771)) 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: 2248.5321 Initial RMS Z values bonds: 14.6461 angles: 0.2076 torsions: N/A planes: 0.1840 non-bonded: 0.0000 chiral vol: 0.0522 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 58) at -355.5101 Final Estimated RMS Z Scores: bonds: 0.0864 angles: 0.1256 torsions: N/A planes: 0.2928 non-bonded: 0.0000 chiral vol: 0.0627 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 196.1940 Refinement elapsed time: 0.0120 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.51471268369434: bond-length-within-tolerance? bond-length 1.51471268369434 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5267486572266 4.8825421333313 19.387336730957)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.2792510986328 6.16372489929199 19.0929470062256)) INFO:: wrote mmCIF "coot-test-ala.cif" INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 67 read successfully DEBUG:: there were 1 types with no dictionary Welcome to Coot WARNING:: bond_restraint_length 4 should be 5 INFO:: created 15 restraints created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 7 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 4835.2158 Initial RMS Z values bonds: 0.0120 angles: 0.0065 torsions: N/A planes: 0.0000 non-bonded: 689.9273 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 45) at -87.3139 Final Estimated RMS Z Scores: bonds: 0.0158 angles: 0.1325 torsions: N/A planes: 0.0141 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 196.4270 Refinement elapsed time: 0.0330 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 68 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_2.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_3.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_6.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_7.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 69 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_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_Mon_Apr__1_12:16:01_2019_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 72 read successfully DEBUG:: there were 0 types with no dictionary in new_molecule_by_residue_type_selection Something bad happened - No residues selected in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 73 read successfully DEBUG:: there were 0 types with no dictionary INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.0000%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.0000%] INFO:: Reading coordinate file: /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 50/87 Molecule 74 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 74 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -3.0000 is_nucleic_acid_flag 0 console_output 1 --------------------------------------------------- INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb > target sequence: ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID ||||||| |||||||||| ||||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| DVSGTVCLSALPPEATDTLNLIAS-DGPFPYSQ-DGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 150.0000 DEBUG:: s.length() 95 DEBUG:: nSelResidues 87 INFO:: backup file coot-backup/_home_paule_data_greg-data_rnase-A-needs-an-insertion.pdb_Mon_Apr__1_12:16:02_2019_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: 138874360 "A" 1 ""] -> ASP [spec: 138874360 "A" 2 ""] -> VAL [spec: 138874360 "A" 3 ""] -> SER [spec: 138874360 "A" 11 ""] -> LEU [spec: 138874360 "A" 12 ""] -> PRO [spec: 138874360 "A" 13 ""] -> PRO [spec: 138874360 "A" 62 ""] -> PRO [spec: 138874360 "A" 63 ""] -> GLY Deletions: [spec: 138874360 "A" 25 ""] [spec: 138874360 "A" 34 ""] Mutations: [spec: 138874360 "A" 24 ""] -> SER [spec: 138874360 "A" 33 ""] -> GLN INFO:: mutate 24 A to a SER INFO:: mutate 33 A to a GLN apply resno updates... Applied 3 insertions Applied 2 mutations Applied 2 deletions INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 75 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:02_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 76 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:02_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3hfl.ent PDB file /home/paule/data/greg-data/pdb3hfl.ent has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 77 read successfully DEBUG:: there were 1 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz 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:: 0.0220 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0140 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:: 0.0010 seconds for contour map INFO:: 0.0390 seconds in total INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.8340 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_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_Mon_Apr__1_12:16:05_2019_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.3260 max devi: 0.5019 min devi: 0.0927 INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/some-waters-with-ter.pdb PDB file /home/paule/data/greg-data/some-waters-with-ter.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 84 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_some-waters-with-ter.pdb_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3.0000,4.0000,5.0000) B-factor: 45.0000 added to molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/tm+some-waters.pdb PDB file /home/paule/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 85 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 2.0000 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3115 INFO:: Using density cut-off: 0.6230 (2.0000 sigma) (mean -0.0337 stdev: 0.1461) 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 = ( 59.91, 3.027, -4.296) is too big to be water INFO:: cluster at xyz = ( 70.01, 19.05, 18.63) is too big to be water INFO:: found 45 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_tm+some-waters.pdb_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 86 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/water-test-no-cell.pdb PDB file /home/paule/data/greg-data/water-test-no-cell.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 87 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_water-test-no-cell.pdb_Mon_Apr__1_12:16:07_2019_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /home/paule/data/greg-data/pathological-water-test.pdb PDB file /home/paule/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 88 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_pathological-water-test.pdb_Mon_Apr__1_12:16:08_2019_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0280 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0510 seconds in total fitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:08_2019_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:08_2019_modification_1.pdb.gz INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.8760,16.1670,23.0330) B-factor: 20.0300 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.1788 rms devi: 4.8592 max devi: 46.2590 min devi: 0.1254 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 91 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 91 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.8760,16.1670,23.0330) B-factor: 20.0300 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.1788 rms devi: 4.8592 max devi: 46.2590 min devi: 0.1254 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:08_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 92 read successfully DEBUG:: there were 0 types with no dictionary 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 93 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 94 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 95 read successfully DEBUG:: there were 1 types with no dictionary ------- 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/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 97 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_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_Mon_Apr__1_12:16:10_2019_modification_1.pdb.gz ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Matching/moving molecule number 100 to 99 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.0353 rms devi: 0.0378 max devi: 0.0545 min devi: 0.0167 INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076) INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) PASS: update monomer restraints Entered testcase - Write mmCIF restraints correctly PASS: Write mmCIF restraints correctly Entered testcase - Refinement OK with zero bond esd PASS: Refinement OK with zero bond esd Entered testcase - Change Chain IDs and Chain Sorting PASS: Change Chain IDs and Chain Sorting Entered testcase - Chain-ids in links change also on change chain id PASS: Chain-ids in links change also on change chain id Entered testcase - Replace Fragment distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) PASS: Replace Fragment Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () PASS: Residues in Region of Residue Entered testcase - Residues in region of a point PASS: Residues in region of a point Entered testcase - Empty molecule on type selection PASS: Empty molecule on type selection Entered testcase - Set Rotamer PASS: Set Rotamer Entered testcase - Rotamer names and scores are correct Rotamer 0 : "m-85" 100.0 Rotamer 1 : "t80" 90.1668395996094 Rotamer 2 : "p90" 50.7077865600586 Rotamer 3 : "m -30 " 21.4231548309326 Rotamer 4 : "m -30 " 21.4231548309326 PASS: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions ::::: (74 "A" 1 "") #f #f ::::: (74 "A" 4 "") #t #t ::::: (74 "A" 57 "") #t #t ::::: (74 "A" 60 "") #f #f ::::: (74 "A" 61 "") #f #f ::::: (74 "A" 92 "") #t #t ::::: (74 "A" 94 "") #f #f results: (#t #t #t #t #t #t #t) PASS: Align and mutate a model with deletions Entered testcase - renumbered residues should be in seqnum order PASS: renumbered residues should be in seqnum order Entered testcase - Autofit Rotamer on Residues with Insertion codes PASS: Autofit Rotamer on Residues with Insertion codes Entered testcase - RNA base has correct residue type after mutation mutated base to type "C" - was "A" mutated base to type "Cr" - was "A" PASS: RNA base has correct residue type after mutation Entered testcase - resname from serial number doesnt crash on silly input PASS: resname from serial number doesnt crash on silly input Entered testcase - DNA bases are the correct residue type after mutation mutated base to type "DC" mutated base to type "DG" mutated base to type "DA" mutated base to type "DT" mutated base to type "Cd" mutated base to type "Gd" mutated base to type "Ad" mutated base to type "Td" PASS: DNA bases are the correct residue type after mutation Entered testcase - SegIDs are correct after mutate PASS: SegIDs are correct after mutate Entered testcase - TER on water chain is removed on adding a water by hand PASS: TER on water chain is removed on adding a water by hand Entered testcase - TER on water chain is removed on adding waters automatically PASS: TER on water chain is removed on adding waters automatically Entered testcase - Adding atoms to Many-Chained Molecule PASS: Adding atoms to Many-Chained Molecule Entered testcase - Arrange waters round protein PASS: Arrange waters round protein Entered testcase - Correct Segid After Add Terminal Residue PASS: Correct Segid After Add Terminal Residue Entered testcase - Correct Segid after NCS residue range copy PASS: Correct Segid after NCS residue range copy Entered testcase - Merge Water Chains PASS: Merge Water Chains Entered testcase - Consolidated merge -------- starting chain list ----------- DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "") DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K") PASS: Consolidated merge Entered testcase - Test for good chain ids after a merge chain-ids: ("AAA" "B" "B-chain") --- chain-ids: ("AAA" "B" "B-chain" "AAA_2") PASS: Test for good chain ids after a merge Entered testcase - LSQ by atom bond-length-within-tolerance? bond-length 0.110921496735531 with target 0.0 and tolerance 0.2 for atom ((" C " "") (1.0 15.5799999237061 " C" "") (56.8940010070801 1.29299998283386 19.6700000762939)) is ((" C " "") (1.0 16.7800006866455 " C" "") (56.8856086730957 1.18242847919464 19.6726627349854)) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 101 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 102 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: spacegroup: P 21 21 21 INFO:: spacegroup: C 1 2 1 INFO:: Matching/moving molecule number 101 to 102 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.5023 rms devi: 0.5938 max devi: 1.6785 min devi: 0.0432 INFO:: Axis orientation: ( 0.567, -0.7175, 0.4046) INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 103 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 104 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/2goz-manip.pdb PDB file /home/paule/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 10/85 Molecule 105 read successfully DEBUG:: there were 7 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 106 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0520 seconds in total masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_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 108 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.3243 34.3243 11.0887 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 41 2 2" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 109 read successfully INFO:: spacegroup: I 41 2 2 LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 110 read successfully Map statistics: mean: -0.0001 st.d: 0.3052 Map statistics: min: -0.7810, max: 6.0791 -0.6953 231 -0.5238 4724 -0.3523 24910 -0.1808 55291 -0.0093 95241 0.1622 40930 0.3337 7480 0.5052 3968 0.6767 2790 0.8482 2117 1.0197 1738 1.1912 1221 1.3628 888 1.5343 595 1.7058 355 1.8773 240 2.0488 137 2.2203 97 2.3918 62 2.5633 46 2.7348 17 2.9063 17 3.0778 13 3.2493 10 3.4208 7 3.5923 1 3.7638 3 3.9353 7 4.1068 2 4.2783 5 4.4498 1 4.6213 2 4.7928 2 4.9643 0 5.1358 1 5.3073 0 5.4788 0 5.6503 0 5.8218 0 5.9933 1 6.1648 0 Map statistics: mean: -0.0000 st.d: 0.0468 Map statistics: min: -0.2115, max: 0.6486 -0.2008 7 -0.1793 48 -0.1578 209 -0.1363 787 -0.1148 2257 -0.0933 5676 -0.0717 12730 -0.0502 24380 -0.0287 38190 -0.0072 46230 0.0143 43880 0.0358 32484 0.0573 19420 0.0788 9718 0.1003 4120 0.1218 1677 0.1433 718 0.1648 329 0.1863 133 0.2078 77 0.2293 29 0.2508 11 0.2723 13 0.2938 8 0.3153 2 0.3368 2 0.3583 2 0.3798 1 0.4013 1 0.4228 2 0.4443 2 0.4658 1 0.4873 1 0.5088 1 0.5304 1 0.5519 1 0.5734 0 0.5949 0 0.6164 0 0.6379 2 0.6594 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 WARNING:: invalid molecule (204050) for write_shelx_ins_file WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. PASS: LSQ by atom Entered testcase - LSQing changes the space-group and cell to that of the reference molecule PASS: LSQing changes the space-group and cell to that of the reference molecule Entered testcase - set-residue-name sets the correct residue PASS: set-residue-name sets the correct residue Entered testcase - fit-protein-make-specs makes all specs specs: 189 ((104 "A" 1 "") (104 "A" 2 "") (104 "A" 3 "") (104 "A" 4 "") (104 "A" 5 "") (104 "A" 6 "") (104 "A" 7 "") (104 "A" 8 "") (104 "A" 9 "") (104 "A" 10 "") (104 "A" 11 "") (104 "A" 12 "") (104 "A" 13 "") (104 "A" 14 "") (104 "A" 15 "") (104 "A" 16 "") (104 "A" 17 "") (104 "A" 18 "") (104 "A" 19 "") (104 "A" 20 "") (104 "A" 21 "") (104 "A" 22 "") (104 "A" 23 "") (104 "A" 24 "") (104 "A" 25 "") (104 "A" 26 "") (104 "A" 27 "") (104 "A" 28 "") (104 "A" 29 "") (104 "A" 30 "") (104 "A" 31 "") (104 "A" 32 "") (104 "A" 33 "") (104 "A" 34 "") (104 "A" 35 "") (104 "A" 36 "") (104 "A" 37 "") (104 "A" 38 "") (104 "A" 39 "") (104 "A" 40 "") (104 "A" 41 "") (104 "A" 42 "") (104 "A" 43 "") (104 "A" 44 "") (104 "A" 45 "") (104 "A" 46 "") (104 "A" 47 "") (104 "A" 48 "") (104 "A" 49 "") (104 "A" 50 "") (104 "A" 51 "") (104 "A" 52 "") (104 "A" 53 "") (104 "A" 54 "") (104 "A" 55 "") (104 "A" 56 "") (104 "A" 57 "") (104 "A" 58 "") (104 "A" 59 "") (104 "A" 60 "") (104 "A" 61 "") (104 "A" 62 "") (104 "A" 63 "") (104 "A" 64 "") (104 "A" 65 "") (104 "A" 66 "") (104 "A" 67 "") (104 "A" 68 "") (104 "A" 69 "") (104 "A" 70 "") (104 "A" 71 "") (104 "A" 72 "") (104 "A" 73 "") (104 "A" 74 "") (104 "A" 75 "") (104 "A" 76 "") (104 "A" 77 "") (104 "A" 78 "") (104 "A" 79 "") (104 "A" 80 "") (104 "A" 81 "") (104 "A" 82 "") (104 "A" 83 "") (104 "A" 84 "") (104 "A" 85 "") (104 "A" 86 "") (104 "A" 87 "") (104 "A" 88 "") (104 "A" 89 "") (104 "A" 90 "") (104 "A" 91 "") (104 "A" 92 "") (104 "A" 93 "") (104 "B" 1 "") (104 "B" 2 "") (104 "B" 3 "") (104 "B" 4 "") (104 "B" 5 "") (104 "B" 6 "") (104 "B" 7 "") (104 "B" 8 "") (104 "B" 9 "") (104 "B" 10 "") (104 "B" 11 "") (104 "B" 12 "") (104 "B" 13 "") (104 "B" 14 "") (104 "B" 15 "") (104 "B" 16 "") (104 "B" 17 "") (104 "B" 18 "") (104 "B" 19 "") (104 "B" 20 "") (104 "B" 21 "") (104 "B" 22 "") (104 "B" 23 "") (104 "B" 24 "") (104 "B" 25 "") (104 "B" 26 "") (104 "B" 27 "") (104 "B" 28 "") (104 "B" 29 "") (104 "B" 30 "") (104 "B" 31 "") (104 "B" 32 "") (104 "B" 33 "") (104 "B" 34 "") (104 "B" 35 "") (104 "B" 36 "") (104 "B" 37 "") (104 "B" 38 "") (104 "B" 39 "") (104 "B" 40 "") (104 "B" 41 "") (104 "B" 42 "") (104 "B" 43 "") (104 "B" 44 "") (104 "B" 45 "") (104 "B" 46 "") (104 "B" 47 "") (104 "B" 48 "") (104 "B" 49 "") (104 "B" 50 "") (104 "B" 51 "") (104 "B" 52 "") (104 "B" 53 "") (104 "B" 54 "") (104 "B" 55 "") (104 "B" 56 "") (104 "B" 57 "") (104 "B" 58 "") (104 "B" 59 "") (104 "B" 60 "") (104 "B" 61 "") (104 "B" 62 "") (104 "B" 63 "") (104 "B" 64 "") (104 "B" 65 "") (104 "B" 66 "") (104 "B" 67 "") (104 "B" 68 "") (104 "B" 69 "") (104 "B" 70 "") (104 "B" 71 "") (104 "B" 72 "") (104 "B" 73 "") (104 "B" 74 "") (104 "B" 75 "") (104 "B" 76 "") (104 "B" 77 "") (104 "B" 78 "") (104 "B" 79 "") (104 "B" 80 "") (104 "B" 81 "") (104 "B" 82 "") (104 "B" 83 "") (104 "B" 84 "") (104 "B" 85 "") (104 "B" 86 "") (104 "B" 87 "") (104 "B" 88 "") (104 "B" 89 "") (104 "B" 90 "") (104 "B" 91 "") (104 "B" 92 "") (104 "B" 93 "") (104 "B" 94 "") (104 "B" 95 "") (104 "B" 96 "")) PASS: fit-protein-make-specs makes all specs Entered testcase - Phosphate distance in pucker analysis is sane PASS: Phosphate distance in pucker analysis is sane Entered testcase - Fix for Oliver Clarke fit by atom selection bug bl: 0.0363726829001203 PASS: Fix for Oliver Clarke fit by atom selection bug Ended 01-pdb+mtz.scm Running 02-shelx.scm ... Entered testcase - Read small molecule .res file PASS: Read small molecule .res file Entered testcase - Read hollander small molecule .res file PASS: Read hollander small molecule .res file Entered testcase - read shelx insulin with fcf PASS: read shelx insulin with fcf Entered testcase - Write an INS from PDB test PASS: Write an INS from PDB test Entered testcafitting terminal residue with 5000 random trials called fit_terminal_residue_generic() residue-seqnum: 2020 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Mon_Apr__1_12:16:13_2019_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_Mon_Apr__1_12:16:13_2019_modification_1.res WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CD2" INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Mon_Apr__1_12:16:13_2019_modification_0.res WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3.0000,-1.0000,60.0000) B-factor: 45.0000 added to molecule INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6000 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3052 INFO:: Using density cut-off: 0.1831 (0.6000 sigma) (mean -0.0203 stdev: 0.1119) INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4000 3.2000 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water INFO:: found 28 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Mon_Apr__1_12:16:13_2019_modification_1.res WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" INFO:: Adding to solvent chain: D LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.1400 83.0300 89.7900 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "P 21 21 21" INFO:: read_file() chain with chain id has 5 residues Symmetry available for this molecule Molecule 115 read successfully LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.0800 32.7600 18.6600 90.0000 101.7300 90.0000 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id has 23 residues Symmetry available for this molecule Molecule 116 read successfully WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " O1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C2 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C5 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" "CL1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " N1 " INFO:: SHELXL file new-horma.ins written. LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL debug:: ## new chain wiith chain-id A INFO:: CELL set to 14.0800 32.7600 18.6600 90.0000 101.7300 90.0000 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id A has 23 residues Symmetry available for this molecule Molecule 117 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.9990 108.9990 107.5550 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 4 2 2" INFO:: read_file() chain with chain id has 4 residues Symmetry available for this molecule Molecule 118 read successfully WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/3GP_from_dict_Mon_Apr__1_12:16:13_2019_modification_0.pdb.gz INFO:: backup file coot-backup/3GP_from_dict_Mon_Apr__1_12:16:13_2019_modification_1.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 120 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:16:13_2019_modification_0.pdb.gz INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb PDB file /home/paule/data/greg-data/test-LIG.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 121 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb PDB file /home/paule/data/greg-data/test-LIG.pdb has been read. INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 122 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 123 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_Mon_Apr__1_12:16:16_2019_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:16_2019_modification_0.pdb.gz ------- resulting_merge_info has size 1 -------- resulting_merge_info[0] [spec: mmdb::MinInt4 "L" 1 ""] INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 125 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:16:16_2019_modification_0.pdb.gz ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 126 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 0/113 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 0/117 INFO:: fill_ghost_info Constructed 6 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain A" Ghost 1 name: "NCS found from matching Chain E onto Chain A" Ghost 2 name: "NCS found from matching Chain G onto Chain A" Ghost 3 name: "NCS found from matching Chain D onto Chain B" Ghost 4 name: "NCS found from matching Chain F onto Chain B" Ghost 5 name: "NCS found from matching Chain H onto Chain B" Molecule 132 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT 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:: 187.4540 seconds to read MTZ file INFO:: 7.1540 seconds to initialize map INFO:: 0.0800 seconds for FFT INFO:: 0.0120 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:: 194.7010 seconds in total INFO:: making difference map from MTZ filename /home/paule/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:: 0.0880 seconds to read MTZ file INFO:: 0.0010 seconds to initialize map INFO:: 0.0780 seconds for FFT INFO:: 0.0110 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.0334 Map maximum: ..... 0.3661 Map minimum: ..... -0.1917 INFO:: 0.0010 seconds for contour map INFO:: 0.1790 seconds in total INFO:: ligand number 0 is molecule number 126 with wiggly flag: 0 in execute_ligand_search_internal() import maps from mol 133 INFO:: Protein centre at: xyz = ( 58.29, 34.65, 30.63) Map statistics: mean: -0.0217 st.d: 0.0886 Map statistics: min: -0.6954, max: 0.7542 -0.6773 6 -0.6411 8 -0.6048 27 -0.5686 116 -0.5324 354 -0.4961 977 -0.4599 1943 -0.4236 3356 -0.3874 5156 -0.3511 6576 -0.3149 7850 -0.2787 8875 -0.2424 9742 -0.2062 11742 -0.1699 16950 -0.1337 29805 -0.0975 58214 -0.0612 102889 -0.0250 142998 0.0113 471776 0.0475 106846 0.0837 56087 0.1200 21597 0.1562 6911 0.1925 2135 0.2287 920 0.2650 467 0.3012 346 0.3374 216 0.3737 118 0.4099 117 0.4462 80 0.4824 50 0.5186 28 0.5549 33 0.5911 15 0.6274 14 0.6636 11 0.6998 2 0.7361 7 0.7723 0 INFO:: find_clusters map_rms is 0.1711 INFO:: Using density cut-off: 0.1711 (1.0000 sigma) (mean -0.0217 stdev: 0.0886) INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4000 3.2000 INFO:: Finding clusters...done debug:: n_ligands_for_cluster() top_score 4.0420 and 4 are decent out of 12 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -50.8108 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 40) at -136.5529 Final Estimated RMS Z Scores: bonds: 0.1074 angles: 0.0375 torsions: N/A planes: 0.0573 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 408.9230 Refinement elapsed time: 0.0340 INFO:: backup file coot-backup/Fitted_ligand_#0-0_Mon_Apr__1_12:19:33_2019_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 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: 17.1202 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 26) at -73.5591 Final Estimated RMS Z Scores: bonds: 0.0457 angles: 0.0446 torsions: N/A planes: 0.0429 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 409.8660 Refinement elapsed time: 0.0940 INFO:: backup file coot-backup/Fitted_ligand_#1-0_Mon_Apr__1_12:19:34_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 12.8997 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 38) at -66.2704 Final Estimated RMS Z Scores: bonds: 0.0572 angles: 0.0249 torsions: N/A planes: 0.0223 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 410.3220 Refinement elapsed time: 0.0150 INFO:: backup file coot-backup/Fitted_ligand_#2-0_Mon_Apr__1_12:19:34_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 34.4825 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 34) at -50.5138 Final Estimated RMS Z Scores: bonds: 0.0557 angles: 0.0295 torsions: N/A planes: 0.0472 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 410.9840 Refinement elapsed time: 0.0210 INFO:: backup file coot-backup/Fitted_ligand_#3-0_Mon_Apr__1_12:19:35_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 51.8558 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 27) at -59.5303 Final Estimated RMS Z Scores: bonds: 0.0792 angles: 0.0310 torsions: N/A planes: 0.0932 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 412.1190 Refinement elapsed time: 0.0650 INFO:: backup file coot-backup/Fitted_ligand_#4-0_Mon_Apr__1_12:19:36_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: -0.4462 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 48) at -117.4501 Final Estimated RMS Z Scores: bonds: 0.0872 angles: 0.0841 torsions: N/A planes: 0.1411 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 413.0340 Refinement elapsed time: 0.0630 INFO:: backup file coot-backup/Fitted_ligand_#5-0_Mon_Apr__1_12:19:37_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 10.7928 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 35) at -74.4890 Final Estimated RMS Z Scores: bonds: 0.0457 angles: 0.0362 torsions: N/A planes: 0.0895 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 413.9170 Refinement elapsed time: 0.0220 INFO:: backup file coot-backup/Fitted_ligand_#6-0_Mon_Apr__1_12:19:38_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 29.7970 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 20) at -60.2968 Final Estimated RMS Z Scores: bonds: 0.0520 angles: 0.0428 torsions: N/A planes: 0.1954 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 414.8240 Refinement elapsed time: 0.0550 INFO:: backup file coot-backup/Fitted_ligand_#7-0_Mon_Apr__1_12:19:39_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 13.4723 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 60) at -92.2098 Final Estimated RMS Z Scores: bonds: 0.1330 angles: 0.1400 torsions: N/A planes: 0.0669 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 415.2760 Refinement elapsed time: 0.1150 INFO:: backup file coot-backup/Fitted_ligand_#8-0_Mon_Apr__1_12:19:39_2019_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 INFO:: created 39 restraints created 15 bond restraints created 22 angle restraints created 2 plane restraints created 0 chiral vol restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 0 bond links 0 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 58 non-bonded restraints calling update_refinement_atoms() initial distortion_score: 21.5046 Initial RMS Z values bonds: 2.3219 angles: 0.0256 torsions: N/A planes: 0.0260 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 41) at -65.4430 Final Estimated RMS Z Scores: bonds: 0.0309 angles: 0.0108 torsions: N/A planes: 0.0708 non-bonded: 0.0000 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 415.8510 Refinement elapsed time: 0.0280 INFO:: backup file coot-backup/Fitted_ligand_#9-0_Mon_Apr__1_12:19:40_2019_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 146 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. dirty mmCIF file? /home/paule/data/greg-data/libcheck_3GP.cif Bad mmdb::mmcif::CIFRC_Ok on ReadMMCIFFile Unknown error. CIF error rc=-13 reason:can't open CIF file init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 148 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 148 storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 148 INFO:: Reading coordinate file: /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb PDB file /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 149 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz 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:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0190 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0520 seconds in total storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 149 Sequence: ?EYTVITPGARTR Confidence: 1.0000 From : HEYTVITPGARTR Chain id: 0 Offset: 53 INFO:: backup file coot-backup/_home_paule_data_greg-data_crashes_on_cootaneering-v2.pdb_Mon_Apr__1_12:19:41_2019_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_Mon_Apr__1_12:19:41_2019_modification_0.pdb.gz ------- resulting_merge_info has size 2 -------- resulting_merge_info[0] {residue-spec-not-set} INFO:: Matching/moving molecule number 153 to 153 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_Mon_Apr__1_12:19:42_2019_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 1, 0.003218, -0.003497| | -0.003225, 1, -0.001985| | 0.003491, 0.001997, 1| ( -24.05, -23.7, -24.44) No unit cell for this molecule, hence no fractional matrix. INFO:: Reading coordinate file: /home/paule/data/greg-data/1wly.pdb PDB file /home/paule/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 154 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/1yb5.pdb PDB file /home/paule/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 324/324 INFO:: NCS chain comparison 0/324 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 155 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 154 has 750 atoms selected INFO:: moving 155 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance(/A) A 6 A 7 A 8 <---> A 2 : 0.7510 A 9 <---> A 3 : 0.9422 A 10 <---> A 4 : 0.6300 A 11 <---> A 5 : 0.7119 A 12 <---> A 6 : 0.6310 A 13 <---> A 7 : 0.4675 A 14 <---> A 8 : 0.4264 A 15 <---> A 9 : 0.9792 A 16 <---> A 10 : 0.7549 A 17 <---> A 11 : 0.4884 A 18 <---> A 12 : 0.7451 A 19 <---> A 13 : 0.4606 A 20 <---> A 14 : 1.2809 A 21 <---> A 15 : 1.2412 A 22 <---> A 16 : 1.0733 A 23 <---> A 17 : 0.9730 A 24 <---> A 18 : 0.4705 A 25 <---> A 19 : 0.3560 A 26 <---> A 20 : 3.1145 A 27 A 28 <---> A 21 : 1.5754 A 29 <---> A 22 : 1.6322 A 30 A 31 <---> A 23 : 1.9973 A 32 <---> A 25 : 1.8324 A 33 <---> A 26 : 0.9310 A 34 <---> A 27 : 0.6808 A 35 <---> A 28 : 0.2674 A 36 <---> A 29 : 0.5995 A 37 <---> A 30 : 0.6992 A 38 <---> A 31 : 0.8620 A 39 <---> A 32 : 0.8421 A 40 <---> A 33 : 0.7208 A 41 <---> A 34 : 0.8681 A 42 <---> A 35 : 0.7781 A 43 <---> A 36 : 0.6211 A 44 <---> A 37 : 0.4657 A 45 <---> A 38 : 0.7475 A 46 <---> A 39 : 0.5170 A 47 <---> A 40 : 0.5058 A 48 <---> A 41 : 0.8897 A 49 <---> A 42 : 0.5835 A 50 <---> A 43 : 0.4347 A 51 <---> A 44 : 0.6192 A 52 <---> A 45 : 0.2150 A 53 <---> A 46 : 0.7474 A 54 <---> A 47 : 1.0213 A 55 <---> A 48 : 0.9208 A 56 <---> A 49 : 0.9392 A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 0.4666 A 66 <---> A 61 : 0.0523 A 67 <---> A 62 : 1.0719 A 68 <---> A 63 : 0.7933 A 69 <---> A 64 : 0.8916 A 70 <---> A 65 : 1.2580 A 71 <---> A 66 : 0.6932 A 72 <---> A 67 : 1.0345 A 73 <---> A 68 : 1.4417 A 74 <---> A 69 : 0.9092 A 75 <---> A 70 : 1.6166 A 76 <---> A 71 : 0.8741 A 77 <---> A 72 : 0.2388 A 78 <---> A 73 : 0.3118 A 79 <---> A 74 : 0.3887 A 80 <---> A 75 : 0.7613 A 81 <---> A 76 : 0.9044 A 82 <---> A 77 : 0.6090 A 83 <---> A 78 : 1.7978 A 84 <---> A 79 : 1.9256 A 85 <---> A 80 : 1.3416 A 86 <---> A 81 : 0.5658 A 87 <---> A 82 : 0.4480 A 88 <---> A 83 : 0.9078 A 89 <---> A 84 : 0.3625 A 90 <---> A 85 : 0.4040 A 91 <---> A 86 : 0.4586 A 92 <---> A 87 : 0.4340 A 93 <---> A 88 : 0.3664 A 94 <---> A 89 : 0.4921 A 95 <---> A 90 : 0.6498 A 96 <---> A 91 : 1.5805 A 97 <---> A 92 : 2.8839 A 98 A 99 A 100 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI INFO:: backup file coot-backup/_home_paule_data_greg-data_1yb5.pdb_Mon_Apr__1_12:19:42_2019_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% WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb se - new molecule by atom selection inherits shelx molecule flag PASS: new molecule by atom selection inherits shelx molecule flag Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy Entered testcase - Add water to SHELX molecule PASS: Add water to SHELX molecule Entered testcase - Find Waters for a SHELXL molecule PASS: Find Waters for a SHELXL molecule Entered testcase - NPD Anisotropic Atom [Mitch Miller] PASS: NPD Anisotropic Atom [Mitch Miller] Entered testcase - close shelx molecules PASS: close shelx molecules Entered testcase - Aniso Bs in P21 b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) PASS: Aniso Bs in P21 Entered testcase - Don't crash on reading a strange HAT file PASS: Don't crash on reading a strange HAT file Ended 02-shelx.scm Running 03-ligand.scm ... Entered testcase - Get monomer test PASS: Get monomer test Entered testcase - Delete all-molecule Hydrogens here 1 PASS: Delete all-molecule Hydrogens Entered testcase - Non-Autoloads PASS: Non-Autoloads Entered testcase - 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 149 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" PASS: Cootaneer Beta Strand Ended 04-cootaneer.scm Running 05-rna-ghosts.scm ... Entered testcase - RNA NCS Ghosts There are 8 residues in chain "A" There are 8 residues in chain "B" PASS: RNA NCS Ghosts Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example PASS: SSM - Frank von Delft's Example Entered testcase - SSM - Alice Dawson's Example 0 "/home/paule/data/greg-data/tutorial-modern.pdb" 2 "/home/paule/data/greg-data/ins-code-fragment-pre.pdb" 3 "/home/paule/data/greg-data/tutorial-modern.pdb" 4 "PTR_from_dict" 5 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 6 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 7 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 8 "test-3hfl.map" 9 "/home/paule/data/greg-data/tutorial-modern.pdb" 10 "mainchain-forward" 11 "/home/paule/data/greg-data/tutorial-modern.pdb" 12 "mainchain-forwards" 13 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 14 "atom selection from tutorial-add-terminal-1-test.pdb" 15 "/home/paule/data/greg-data/frag-2wot.pdb" 16 "/home/paule/data/greg-data/tutorial-modern.pdb" 17 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 18 "sphere selection from tutorial-modern.pdb" 20 "/home/paule/data/greg-data/rotamer-test-fragment.pdb" 21 "/home/paule/data/greg-data/res098.pdb" 22 "/home/paule/data/greg-data/tutorial-modern.pdb" 23 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 24 "/home/paule/data/greg-data/pdb3knw.ent" 25 "/home/paule/data/greg-data/pdb1py3.ent" 28 "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb" 29 "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 32 "/home/paule/data/greg-data/tutorial-modern.pdb" 33 "atom selection from tutorial-modern.pdb" 34 "/home/paule/data/greg-data/tutorial-modern.pdb" 35 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 36 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 37 "/home/paule/data/greg-data/tutorial-modern.pdb" 38 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 39 "/home/paule/data/greg-data/tutorial-modern.pdb" 40 "/home/paule/data/greg-data/alt-conf-waters.pdb" 41 "/home/paule/data/greg-data/backrub-fragment.pdb" 42 "Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb" 43 "/home/paule/data/greg-data/coords-B3A.pdb" 44 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 45 "/home/paule/data/greg-data/test-TER-OXT.pdb" 46 "/home/paule/data/greg-data/val.pdb" 47 "/home/paule/data/greg-data/2yie-frag.pdb" 48 "/home/paule/data/greg-data/4f8g.pdb" 49 "/home/paule/data/greg-data/4f8g.pdb" 50 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 51 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 52 "/home/paule/data/greg-data/tutorial-modern.pdb" 53 "Generic Masked Map" 54 "difference-map" 57 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 58 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 59 "averaged-map" 60 "difference-map" 61 "/home/paule/data/greg-data/multi-carbo-coot-3.pdb" 62 "/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb" 63 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 64 "/home/paule/data/greg-data/monomer-VAL.pdb" 65 "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 66 "atom selection from tutorial-modern.pdb" 67 "/home/paule/data/greg-data/monomer-ACT.pdb" 68 "/home/paule/data/greg-data/tutorial-modern.pdb" 69 "/home/paule/data/greg-data/tutorial-modern.pdb" 70 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 71 "atom selection from tutorial-modern.pdb" 72 "/home/paule/data/greg-data/tutorial-modern.pdb" 73 "/home/paule/data/greg-data/tutorial-modern.pdb" 74 "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb" 75 "/home/paule/data/greg-data/tutorial-modern.pdb" 76 "/home/paule/data/greg-data/tutorial-modern.pdb" 77 "/home/paule/data/greg-data/pdb3hfl.ent" 78 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 79 "Ideal-A-form-RNA" 80 "Ideal-A-form-RNA" 81 "Ideal-A-form-DNA" 82 "Ideal-A-form-DNA" 83 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 84 "/home/paule/data/greg-data/some-waters-with-ter.pdb" 85 "/home/paule/data/greg-data/tm+some-waters.pdb" 86 "/home/paule/data/greg-data/tutorial-modern.pdb" 87 "/home/paule/data/greg-data/water-test-no-cell.pdb" 88 "/home/paule/data/greg-data/pathological-water-test.pdb" 89 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 90 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 91 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 92 "/home/paule/data/greg-data/tutorial-modern.pdb" 93 "/home/paule/data/greg-data/pdb1hvv.ent" 94 "/home/paule/data/greg-data/monomer-ACT.pdb" 95 "/home/paule/data/greg-data/monomer-NPO.pdb" 96 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_93" 97 "/home/paule/data/greg-data/tutorial-modern.pdb" 98 "atom selection from tutorial-modern.pdb" 99 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 100 returing from do_Ca_or_P_bonds_internal() with atom_centres size 0 INFO:: Reading coordinate file: /home/paule/data/greg-data/2qd9.pdb PDB file /home/paule/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 156 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/2gtn.pdb PDB file /home/paule/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 0/337 Molecule 157 read successfully DEBUG:: there were 1 types with no dictionary INFO:: reference 156 has 169 atoms selected INFO:: moving 157 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_home_paule_data_greg-data_2gtn.pdb_Mon_Apr__1_12:19:43_2019_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 158 read successfully INFO:: making map from mtz filename /home/paule/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:: 0.0280 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0200 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0010 seconds for contour map INFO:: 0.0510 seconds in total INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.8760,16.1670,23.0330) B-factor: 20.0300 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.1788 rms devi: 4.8592 max devi: 46.2590 min devi: 0.1254 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: installing ghost map with name :Map 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:: 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 INFO:: installing ghost map with name :Map 159 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0004 st.d: 0.3236 Map statistics: min: -1.4496, max: 2.3411 -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 2 2.3885 0 no diffs NCS target chain has 93 peers. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 164 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_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: 164 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 164 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 164 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 164 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_modification_5.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1t6q.ent PDB file /home/paule/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 165 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_Apr__1_12:19:44_2019_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: 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 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_Apr__1_12:19:44_2019_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_Apr__1_12:19:44_2019_modification_2.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 166 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 166 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 167 to 166 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Mon_Apr__1_12:19:44_2019_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 168 to 166 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.1943 rms devi: 0.2112 max devi: 0.3583 min devi: 0.0329 INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095) INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Mon_Apr__1_12:19:44_2019_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 169 to 166 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.4174 rms devi: 0.4531 max devi: 0.7926 min devi: 0.0759 INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411) INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Mon_Apr__1_12:19:44_2019_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 170 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/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:: 11.3040 seconds to read MTZ file INFO:: 0.0220 seconds to initialize map INFO:: 0.0330 seconds for FFT INFO:: 0.0040 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:: 11.3630 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 171 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 171 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 171 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 171 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 171 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 171 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 171 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 171 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 171 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 error (syntax error) error (syntax error) error (not syntax error) Traceback (most recent call last): File "", line 1, in NameError: name 'rr_not_found_thing' is not defined "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 101 "/home/paule/data/greg-data/tutorial-modern.pdb" 102 "/home/paule/data/greg-data/pdb1py3.ent" 103 "/home/paule/data/greg-data/tutorial-modern.pdb" 104 "/home/paule/data/greg-data/tutorial-modern.pdb" 105 "/home/paule/data/greg-data/2goz-manip.pdb" 106 "/home/paule/data/greg-data/tutorial-modern.pdb" 107 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 108 "/home/paule/data/greg-data/HOF.RES" 109 "/home/paule/data/greg-data/hollander.ins" 112 "/home/paule/data/greg-data/insulin.fcf Diff-SigmaA" 113 "atom selection from insulin.res" 114 "atom selection from insulin.res" 116 "/home/paule/data/greg-data/horma-p21.res" 117 "new-horma.ins" 118 "/home/paule/data/greg-data/crash.hat" 119 "3GP_from_dict" 120 "/home/paule/data/greg-data/monomer-3GP.pdb" 121 "/home/paule/data/greg-data/test-LIG.pdb" 122 "/home/paule/data/greg-data/test-LIG.pdb" 123 "/home/paule/data/greg-data/tutorial-modern.pdb" 124 "3GP_from_dict" 125 "/home/paule/data/greg-data/monomer-3GP.pdb" 126 "/home/paule/data/greg-data/monomer-NPO.pdb" 127 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 128 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 129 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 130 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 131 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 132 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 133 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 134 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 135 "Masked (by protein)" 136 "Fitted ligand #0-0" 137 "Fitted ligand #1-0" 138 "Fitted ligand #2-0" 139 "Fitted ligand #3-0" 140 "Fitted ligand #4-0" 141 "Fitted ligand #5-0" 142 "Fitted ligand #6-0" 143 "Fitted ligand #7-0" 144 "Fitted ligand #8-0" 145 "Fitted ligand #9-0" 146 "/home/paule/data/greg-data/monomer-3GP.pdb" 147 "Copy_of_/home/paule/data/greg-data/monomer-3GP.pdb" 148 "/home/paule/data/greg-data/tutorial-modern.pdb" 149 "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb" 150 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 151 "Ideal-A-form-RNA" 154 "/home/paule/data/greg-data/1wly.pdb" 155 "/home/paule/data/greg-data/1yb5.pdb" PASS: SSM - Alice Dawson's Example Entered testcase - SSM by atom selection [JED Example] PASS: SSM by atom selection [JED Example] Ended 06-ssm.scm Running 07-ncs.scm ... Entered testcase - NCS maps test PASS: NCS maps test Entered testcase - NCS chains info NCS info: (("A" "B")) PASS: NCS chains info Entered testcase - NCS deviation info PASS: NCS deviation info Entered testcase - NCS Residue Range copy PASS: NCS Residue Range copy Entered testcase - NCS Residue Range edit to all chains result: (#t #t) PASS: NCS Residue Range edit to all chains Entered testcase - Manual NCS ghosts generates correct NCS chain ids NCS ghost chain IDs pre: (("B" "A" "C" "D")) NCS ghost chain IDs post: (("B" "A" "C" "D")) PASS: Manual NCS ghosts generates correct NCS chain ids Entered testcase - NCS maps overwrite existing maps ==== test-name: "Map 171 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 171 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 171 NCS found from matching Chain D onto Chain A" n-matchers: 2 PASS: NCS maps overwrite existing maps Ended 07-ncs.scm Running 08-utils.scm ... Entered testcase - Test key symbols WARNING:: could not find key-sym-code for "missing key" PASS: Test key symbols Entered testcase - Test running a Python function test_val_2 passed test_val_3 passed PASS: Test running a Python function Entered testcase - Internal/External Molecule Numbers match PAINFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 180 read successfully DEBUG:: there were 0 types with no dictionary Entering test: OXT in restraints? INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/ There are 135 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/n/NA.cif There are 2 data in /home/paule/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.1414 PASS: test symm trans to origin Entering test: test lsq plane LSQ deviations: 0.0000 0.0000 PASS: test lsq plane Entering test: test COO modification INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/ There are 135 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/n/NA.cif INFO:: Reading coordinate file: /home/paule/data/greg-data/hideous-OXT.pdb PDB file /home/paule/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom created 7 bond restraints created 8 angle restraints created 1 plane restraints created 1 chiral vol restraints created 2 torsion restraints created 23 restraints INFO:: make_restraints(): made 13 non-bonded restraints initial distortion_score: 1241.5407 Initial RMS Z values bonds: 3.7208 angles: 7.4688 torsions: 0.2764 planes: 16.9011 non-bonded: 0.0000 chiral vol: 1.2266 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 243) at 0.0349 Final Estimated RMS Z Scores: bonds: 0.0017 angles: 0.0239 torsions: 0.1205 planes: 0.0019 non-bonded: 0.0000 chiral vol: 0.0068 rama plot: N/A start_pos: N/A GemanMcCl: N/A refinement_took 0.0060 seconds OXT out of plane distance: 0.0000 OXT->O distance: 2.1104 PASS: test COO modification Entering test: remove whitespace PASS: remove whitespace Entering test: New comp_ids are sane PASS: New comp_ids are sane Entering test: Remove Trailing Slash PASS: Remove Trailing Slash Entering test: Residues for phi,psi are close enough to be considered linked INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 bad residues for phi,psi calculation bad residues for phi,psi calculation PASS: Residues for phi,psi are close enough to be considered linked SS: 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 128 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 1 # of unresolved testcases 1 # 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 128 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 1 # of unresolved testcases 1 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 ObjectCache: Leaked 0005 refs to

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

ObjectCache: Leaked 0004 refs to Guile 1.8.8 Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation Guile may be distributed under the terms of the GNU General Public Licence; certain other uses are permitted as well. For details, see the file `COPYING', which is included in the Guile distribution. There is no warranty, to the extent permitted by law. catching the crash log: (coot-crash-catcher.scm:5163): Gtk-WARNING **: cannot open display: test_coot: coot test failed