testing with greg testing with greg currently we are here: /home/paule/autobuild/building/ubuntu-server_2018-01-02__T23_29_02/coot-0.8.9-pre Tue Jan 2 23:43:42 GMT 2018 WARNING:: ccp4 setup file setup-ccp4 does not exist. /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ INFO:: Reading coordinate file: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/paule/autobuild/Linux-ubuntu-server-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-ubuntu-server-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Evening Paul, Welcome to Coot version 0.8.9-pre (set-display-intro-string "Good Evening Paul, Welcome to Coot version 0.8.9-pre") (use-graphics-interface-state) (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good evening root. Welcome to Coot 0.8.9-pre") (set-display-lists-for-maps 0) (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run command-line-greg.scm INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary Molecule number -5 is not a valid model molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/2WF6.cif mmCIF file /home/paule/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 1 read successfully DEBUG:: there were 3 types with no dictionary in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Reading coordinate file: /home/paule/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/paule/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file 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_Tue_Jan__2_23:43:45_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jan__2_23:43:45_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jan__2_23:43:45_2018_modification_2.pdb.gz WARNING:: Error reading bogus.map Read map bogus.map failed WARNING:: Can't find file bogus.mtz INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.042 seconds to read MTZ file INFO:: 0.018 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.022 seconds for contour map INFO:: 0.109 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.024 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.02 seconds for contour map INFO:: 0.071 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 80, 108, 108) INFO:: 0.037 seconds to read MTZ file INFO:: 0.01 seconds to initialize map INFO:: 0.019 seconds for FFT INFO:: 0.005 seconds for statistics Map mean: ........ 6.46373e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.81878 Map minimum: ..... -1.02352 INFO:: 0.004 seconds for contour map INFO:: 0.075 seconds in total INFO:: map file type was determined to be CCP4 type INFO:: attempting to read CCP4 map: test-3hfl.map closing CCP4 map: test-3hfl.map Map statistics: mean: 6.46373e-11 st.d: 0.260405 Map statistics: min: -1.02352, max: 1.81878 -0.987993 5 -0.916935 16 -0.845877 73 -0.77482 214 -0.703762 683 -0.632705 1662 -0.561647 3458 -0.49059 6630 -0.419532 10974 -0.348475 16784 -0.277417 24050 -0.20636 35976 -0.135302 52684 -0.0642446 70826 0.00681294 75511 0.0778705 59049 0.148928 33738 0.219986 17844 0.291043 11108 0.362101 8875 0.433158 7682 0.504216 6862 0.575273 5661 0.646331 4738 0.717388 3751 0.788446 2781 0.859503 1898 0.930561 1313 1.00162 799 1.07268 428 1.14373 224 1.21479 120 1.28585 55 1.35691 44 1.42796 20 1.49902 9 1.57008 7 1.64114 4 1.71219 3 1.78325 1 1.85431 0 INFO:: n grid points: 466560 INFO:: mean before filtering: 6.46373e-11 INFO:: variance before filtering: 0.0678109 INFO:: filter by ignoring 364 of 466560 counts ( = 0.07802%) with values around -0.03426 from bin 3480 of 10000 Map mean: ........ 2.69e-05 Map rmsd: ........ 0.2605 Map maximum: ..... 1.819 Map minimum: ..... -1.024 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 7 read successfully DEBUG:: there were 0 types with no dictionary /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /home/paule/autobuild/Linux-ubuntu-server-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-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb INFO:: 8375 fragments found in total of which 0 were 5 peptides 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-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 9 read successfully DEBUG:: there were 0 types with no dictionary fitting terminal residue with 1000 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_Tue_Jan__2_23:43:47_2018_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Tue_Jan__2_23:43:47_2018_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 11 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:43:47_2018_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:43:47_2018_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:43:47_2018_modification_2.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/rotamer-test-fragment.pdb PDB file /home/paule/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 14 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] INFO:: Reading coordinate file: /home/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 15 read successfully DEBUG:: there were 0 types with no dictionary created 6 bond restraints created 6 angle restraints created 0 plane restraints created 1 chiral vol restraints created 13 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 9 non-bonded restraints initial distortion_score: 26.65 Initial RMS Z values bonds: 0.2292 angles: 0.4339 torsions: N/A planes: 0.3222 non-bonded: 0 chiral vol: 0.1627 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 149) at 9.945 Final Estimated RMS Z Scores: bonds: 0.09591 angles: 0.6652 torsions: N/A planes: 0.6486 non-bonded: 0 chiral vol: 0.5914 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.284 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Tue_Jan__2_23:43:48_2018_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 16 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.023 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.023 seconds for contour map INFO:: 0.073 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:48_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:48_2018_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.93 INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3knw.ent PDB file /home/paule/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 185/199 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 18 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3knw.ent_Tue_Jan__2_23:43:48_2018_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 19 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_Tue_Jan__2_23:43:49_2018_modification_0.pdb.gz INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP Good evening root. Welcome to Coot 0.8.9-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 - 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 - Set Atom Attribute Test PASS: Set Atom Attribute Test Entered testcase - Add Terminal Residue Test PASS: Add Terminal Residue Test Entered testcase - Adding residue by phi psi, no crash PASS: Adding residue by phi psi, no crash Entered testcase - Select by Sphere Sphere mol: there are 4 residues in chain "B" Found 20 sphere atoms PASS: Select by Sphere Entered testcase - Test Views PASS: Test Views Entered testcase - Label Atoms and Delete PASS: Label Atoms and Delete Entered testcase - Rotamer outliers PASS: Rotamer outliers Entered testcase - Alt Conf Occ Sum Reset For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 PASS: Alt Conf Occ Sum Reset Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue PASS: Correct occupancies after auto-fit rotamer on alt-confed residue Entered testcase - Rotamers work on MSE se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746)) se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616)) PASS: Rotamers work on MSE Entered testcase - 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 20 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.023 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.022 seconds for FFT INFO:: 0.005 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.021 seconds for contour map INFO:: 0.071 seconds in total DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:49_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/paule/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 22 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_Tue_Jan__2_23:43:49_2018_modification_0.pdb.gz flipped 65 A 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 23 read successfully DEBUG:: there were 0 types with no dictionary in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x4bf57c0 omega: 1 12.77 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:43:49_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:43:49_2018_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 flipped 11 A INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:43:49_2018_modification_2.pdb.gz created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 4 angle links 2 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 27 non-bonded restraints initial distortion_score: 5128 Initial RMS Z values bonds: 15.46 angles: 7.124 torsions: N/A planes: 2.181 non-bonded: 126.2 chiral vol: 3.045 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 55) at -3317 Final Estimated RMS Z Scores: bonds: 0.5792 angles: 0.7617 torsions: N/A planes: 2.372 non-bonded: 0.05013 chiral vol: 0.4185 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.428 Refinement elapsed time: 0.015 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:43:49_2018_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_Tue_Jan__2_23:43:49_2018_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:43:49_2018_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.648 created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 4 angle links 2 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 63 non-bonded restraints initial distortion_score: -3565 Initial RMS Z values bonds: 0.9124 angles: 1.705 torsions: N/A planes: 3.183 non-bonded: 0.1617 chiral vol: 0.4899 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 39) at -3690 Final Estimated RMS Z Scores: bonds: 0.5259 angles: 0.6863 torsions: N/A planes: 2.446 non-bonded: 0.0231 chiral vol: 0.2681 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.518 Refinement elapsed time: 0.016 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:43:49_2018_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 24 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.023 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.024 seconds for FFT INFO:: 0.005 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.021 seconds for contour map INFO:: 0.073 seconds in total created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 6 non-bonded restraints initial distortion_score: -1606 Initial RMS Z values bonds: 1.674 angles: 1.07 torsions: N/A planes: 0.6113 non-bonded: 9.246 chiral vol: 1.462 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 60) at -1725 Final Estimated RMS Z Scores: bonds: 1.085 angles: 1.211 torsions: N/A planes: 0.5676 non-bonded: 0.04711 chiral vol: 1.664 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.762 Refinement elapsed time: 0.009 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:50_2018_modification_0.pdb.gz INFO:: replace_coords: 6 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 26 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_Tue_Jan__2_23:43:50_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: created 81 restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints 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 1979 non-bonded restraints initial distortion_score: -8724 Initial RMS Z values bonds: 1.743 angles: 1.268 torsions: N/A planes: 0.8383 non-bonded: 0.0005336 chiral vol: 0.8944 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 4) at -9017 Final Estimated RMS Z Scores: bonds: 0.5818 angles: 0.6239 torsions: N/A planes: 0.6282 non-bonded: 2.481e-05 chiral vol: 0.2426 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.081 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jan__2_23:43:50_2018_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 1393 non-bonded restraints initial distortion_score: -661 Initial RMS Z values bonds: 0.9807 angles: 1.018 torsions: N/A planes: 1.787 non-bonded: 4.74 chiral vol: 10.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -8498 Final Estimated RMS Z Scores: bonds: 1.195 angles: 1.359 torsions: N/A planes: 1.851 non-bonded: 0.01281 chiral vol: 1.09 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.368 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jan__2_23:43:50_2018_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 27 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.023 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.021 seconds for contour map INFO:: 0.071 seconds in total created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -1571 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 1.985 non-bonded: 11.39 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 53) at -7364 Final Estimated RMS Z Scores: bonds: 1.112 angles: 1.076 torsions: N/A planes: 0.8775 non-bonded: 0.02141 chiral vol: 0.7854 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.673 Refinement elapsed time: 0.088 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 29 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_Tue_Jan__2_23:43:51_2018_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring 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 30 read successfully DEBUG:: there were 0 types with no dictionary INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3626 rms devi: 0.4561 max devi: 2.14 min devi: 0.07863 find_ncs_matrix returns (LSQ) | 0.9705, -0.04709, -0.2363| | 0.2357, 0.3883, 0.8909| | 0.04978, -0.9203, 0.388| ( 37.8, -17.17, 13.85) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Tue_Jan__2_23:43:51_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Tue_Jan__2_23:43:51_2018_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/coords-B3A.pdb PDB file /home/paule/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 32 read successfully DEBUG:: there were 1 types with no dictionary created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 2.951 Initial RMS Z values bonds: 0.6619 angles: 0.3737 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.25 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 23) at 4.802e-05 Final Estimated RMS Z Scores: bonds: 0.001418 angles: 0.002701 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.001214 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.203 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Tue_Jan__2_23:43:51_2018_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. dirty mmCIF file? /home/paule/data/greg-data/lib-B3A.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/lib-B3A.cif had no bond restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 4.802e-05 Initial RMS Z values bonds: 0.001418 angles: 0.002701 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.001214 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at 3.529e-05 Final Estimated RMS Z Scores: bonds: 0.0003425 angles: 0.002614 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0007295 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.347 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Tue_Jan__2_23:43:51_2018_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. Welcome to Coot created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 3.018 Initial RMS Z values bonds: 0.6708 angles: 0.3753 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.2536 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 16) at 1.587e-06 Final Estimated RMS Z Scores: bonds: 0.0003952 angles: 0.0003942 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0001708 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.493 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Tue_Jan__2_23:43:51_2018_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 Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.024 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.02 seconds for contour map INFO:: 0.071 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. No Spacegroup found for this PDB file 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 34 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_test-TER-OXT.pdb_Tue_Jan__2_23:43:51_2018_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.13,-9.09,14.92) B-factor: 45 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. No Spacegroup found for this PDB file 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 35 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_Tue_Jan__2_23:43:52_2018_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/2yie-frag.pdb PDB file /home/paule/data/greg-data/2yie-frag.pdb has been read. No Spacegroup found for this PDB file 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 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_2yie-frag.pdb_Tue_Jan__2_23:43:52_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04043 rms devi: 0.04717 max devi: 0.08328 min devi: 0.01301 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 37 read successfully DEBUG:: there were 1 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Tue_Jan__2_23:43:52_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04346 rms devi: 0.04779 max devi: 0.07399 min devi: 0.01477 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 38 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Tue_Jan__2_23:43:52_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.03945 rms devi: 0.04446 max devi: 0.06949 min devi: 0.01513 INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.024 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.018 seconds for contour map INFO:: 0.069 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.023 seconds to read MTZ file INFO:: 0.032 seconds to initialize map INFO:: 0.037 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 1.185e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.029 seconds for contour map INFO:: 0.128 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 41 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.001404 st.d: 0.3055 Map statistics: min: -0.8957, max: 2.764 -0.85 7 -0.7585 47 -0.667 345 -0.5755 1966 -0.484 7547 -0.3926 21145 -0.3011 36984 -0.2096 49747 -0.1181 62502 -0.02661 78146 0.06488 56227 0.1564 31741 0.2479 15372 0.3393 9396 0.4308 7278 0.5223 6354 0.6138 5287 0.7053 4622 0.7968 3865 0.8883 3168 0.9798 2366 1.071 1769 1.163 1258 1.254 879 1.346 637 1.437 417 1.529 237 1.62 135 1.712 69 1.803 46 1.895 18 1.986 8 2.078 2 2.169 6 2.261 2 2.352 0 2.444 1 2.535 3 2.627 0 2.718 1 2.81 0 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 CISPEPs: "3" PASS: Correction of CISPEP test Entered testcase - Refine Zone with Alt conf refined moved: d=0.702068814082454 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.28288458381387 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 1.112" 1.11162889003754) ("Angles" "Angles: 1.076" 1.07647943496704) ("Planes" "Planes: 0.877" 0.877498030662537) ("Non-bonded" "Non-bonded: 0.146" 0.146322458982468) ("Chirals" "Chirals: 0.785" 0.785365402698517))) ow factor: 0.962742939591408 PASS: Refinement gives useful results Entered testcase - Rigid Body Refine Alt Conf Waters PASS: Rigid Body Refine Alt Conf Waters Entered testcase - Setting multiple atom attributes PASS: Setting multiple atom attributes Entered testcase - Tweak Alt Confs on Active Residue PASS: Tweak Alt Confs on Active Residue Entered testcase - Backrub rotamer PASS: Backrub rotamer Entered testcase - Libcif horne PASS: Libcif horne Entered testcase - Refmac Parameters Storage PASS: Refmac Parameters Storage Entered testcase - OXT is added before TER record - add only one found TER "TER 25 ASP A 14 " PASS: OXT is added before TER record - add only one Entered testcase - The position of the oxygen after a mutation PASS: The position of the oxygen after a mutation Entered testcase - TER is at the end of a nucleotide after mutation PASS: TER is at the end of a nucleotide after mutation Entered testcase - C7 is removed on mutation from a DC PASS: C7 is removed on mutation from a DC Entered testcase - C7 is added on mutation to a DC DEBUG:: atoms is (" P " " OP1" " OP2" " O5'" " C5'" " C4'" " O4'" " C3'" " O3'" " C2'" " C1'" " N1 " " C2 " " N3 " " C4 " " C5 " " C6 " " O2 " " O4 " " C7 ") PASS: C7 is added on mutation to a DC Entered testcase - Mask and difference map high-values: (0.966407895088196 0.928917825222015 0.952126145362854 0.646193742752075 0.637681543827057 0.801941633224487 0.734838247299194 1.07139241695404 0.994847536087036 0.931116282939911 0.78803938627243) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) Map statistics: mean: -0.001364 st.d: 0.06029 Map statistics: min: -2.977, max: 0.7461 -2.931 1 -2.838 1 -2.744 1 -2.651 2 -2.558 2 -2.465 0 -2.372 2 -2.279 1 -2.186 1 -2.093 4 -2 2 -1.907 3 -1.814 4 -1.721 4 -1.627 8 -1.534 11 -1.441 15 -1.348 33 -1.255 33 -1.162 49 -1.069 65 -0.9759 120 -0.8828 145 -0.7898 159 -0.6967 202 -0.6036 249 -0.5105 275 -0.4174 291 -0.3243 411 -0.2313 440 -0.1382 581 -0.0451 300752 0.04798 101991 0.1411 1213 0.2341 1098 0.3272 767 0.4203 463 0.5134 156 0.6065 36 0.6995 8 0.7926 1 diff-high-values: (0.00350911822170019 -6.19744881987572e-4 0.00425338884815574 0.00702545186504722 0.00246794405393302 0.0033501957077533 0.00518705137073994 0.00365039915777743 0.00318349059671164 0.00567070674151182 0.00321404589340091) diff-low-values: (-0.869144320487976 -0.88269180059433 -1.18596041202545 -1.16333603858948 -1.04177522659302 -0.848253965377808 -0.827702522277832 -0.704876363277435 -0.9398592710495 -0.532725632190704) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 44 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.024 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.021 seconds for contour map INFO:: 0.072 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.023 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.022 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 9.022e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.021 seconds for contour map INFO:: 0.071 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.023 seconds to read MTZ file INFO:: 0.045 seconds to initialize map INFO:: 0.046 seconds for FFT INFO:: 0.011 seconds for statistics Map mean: ........ 1.146e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.071 Map minimum: ..... -0.8775 INFO:: 0.049 seconds for contour map INFO:: 0.174 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 128, 160, 80) by 1 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1 Map statistics: mean: 1.688e-07 st.d: 0.3111 Map statistics: min: -0.8941, max: 3.007 -0.8453 8 -0.7478 64 -0.6503 542 -0.5527 3067 -0.4552 12045 -0.3577 29986 -0.2601 46658 -0.1626 61563 -0.06508 73639 0.03245 68489 0.13 41912 0.2275 19494 0.325 11050 0.4226 8221 0.5201 7074 0.6176 5839 0.7152 5071 0.8127 4183 0.9102 3295 1.008 2384 1.105 1722 1.203 1175 1.3 843 1.398 560 1.495 325 1.593 179 1.69 90 1.788 59 1.886 23 1.983 9 2.081 8 2.178 6 2.276 2 2.373 2 2.471 4 2.568 3 2.666 2 2.763 2 2.861 1 2.958 0 3.056 1 Map statistics: mean: -1.679e-07 st.d: 0.001076 Map statistics: min: -0.01094, max: 0.0109 -0.01067 1 -0.01012 1 -0.009578 0 -0.009032 1 -0.008485 3 -0.007939 2 -0.007393 4 -0.006847 7 -0.006301 25 -0.005755 37 -0.005208 103 -0.004662 260 -0.004116 640 -0.00357 1269 -0.003024 2611 -0.002478 5434 -0.001931 10529 -0.001385 21799 -0.0008391 51978 -0.000293 109495 0.0002532 110465 0.0007994 52013 0.001346 20447 0.001892 9606 0.002438 5236 0.002984 2974 0.00353 1857 0.004076 1167 0.004622 683 0.005169 388 0.005715 223 0.006261 139 0.006807 86 0.007353 56 0.007899 25 0.008446 16 0.008992 7 0.009538 4 0.01008 4 0.01063 4 0.01118 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 50 read successfully DEBUG:: there were 2 types with no dictionary created 46 bond restraints created 82 angle restraints created 2 plane restraints created 8 chiral vol restraints created 138 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A INFO:: glycosidic_linkage type :ALPHA1-4: Link restraints: 1 bond links 3 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 750 non-bonded restraints initial distortion_score: 2652 Initial RMS Z values bonds: 6.162 angles: 2.853 torsions: N/A planes: 0.08353 non-bonded: 0.2254 chiral vol: 0.9035 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 887) at 15.99 Final Estimated RMS Z Scores: bonds: 0.1009 angles: 0.4225 torsions: N/A planes: 0.0264 non-bonded: 0.0001898 chiral vol: 0.1561 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.243 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-3.pdb_Tue_Jan__2_23:43:54_2018_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 0.311081498861313 and diff-map: 0.0010762547608465 PASS: Simple Averaged maps Entered testcase - Make a glycosidic linkage bond-length: 2.2472998823295: bond-length: 1.44437928674295: bond-length-within-tolerance? bond-length 1.44437928674295 with target 1.439 and tolerance 0.04 for atom ((" O4 " "") (1.0 20.0 " O" "") (-3.95734977722168 20.753511428833 1.51749432086945)) is ((" C1 " "") (1.0 20.0 " C" "") (-3.19250345230103 21.6129570007324 2.39076113700867)) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb PDB file /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 3 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 4/110 Molecule 51 read successfully DEBUG:: there were 1 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.023 seconds to read MTZ file INFO:: 0.011 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.041e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.015 seconds for contour map INFO:: 0.068 seconds in total ......... checking for /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab ..that failed - trying /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/NAG-decorations.tab INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:43:55_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:43:55_2018_modification_1.pdb.gz INFO:: link torsion generated from link bond restraint INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:43:55_2018_modification_2.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 929 non-bonded restraints ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 initial distortion_score: 6.746e+04 Initial RMS Z values bonds: 0.3607 angles: 0.6064 torsions: N/A planes: 0.6834 non-bonded: 72.81 chiral vol: 0.4449 rama plot: N/A start_pos: N/A GemanMcCl: N/A ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 Minimum found (iteration number 66) at -69.72 Final Estimated RMS Z Scores: bonds: 2.523 angles: 1.926 torsions: N/A planes: 2.463 non-bonded: 0.05964 chiral vol: 1.387 rama plot: N/A start_pos: N/A GemanMcCl: N/A ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 SUCCESS TIME:: (dragged refinement): 10.37 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:43:55_2018_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 674 non-bonded restraints ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 initial distortion_score: -69.72 Initial RMS Z values bonds: 2.523 angles: 1.926 torsions: N/A planes: 2.463 non-bonded: 0.0822 chiral vol: 1.387 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at -69.72 Final Estimated RMS Z Scores: bonds: 2.523 angles: 1.926 torsions: N/A planes: 2.463 non-bonded: 0.0822 chiral vol: 1.387 rama plot: N/A start_pos: N/A GemanMcCl: N/A ERROR:: in add_link_bond_templ() bad atom indexing 1 ERROR:: in add_link_bond_templ() bad atom indexing 2 SUCCESS TIME:: (dragged refinement): 10.42 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:43:55_2018_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. PASS: Make a glycosidic linkage Entered testcase - Refine an NAG-ASN Link bond-length-within-tolerance? bond-length 1.57908172598079 with target 1.43 and tolerance 0.2 for atom ((" ND2" "") (1.0 16.9300003051758 " N" "") (-14.0945720672607 -0.0967348963022232 -7.57974481582642)) is ((" C1 " "") (1.0 45.0 " C" "") (-12.6736936569214 -0.444832026958466 -6.98524332046509)) 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 53 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 1 CB created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.997 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0 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: 0.01222 angles: 0.09486 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1454 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 10.79 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:43:56_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 53 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:43:56_2018_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:43:56_2018_modification_0.pdb.gz PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:43:56_2018_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.997 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0 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: 0.01222 angles: 0.09486 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1454 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 10.81 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:43:56_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. PASS: Refine an NAG-ASN Link Entered testcase - Test for flying hydrogens on undo bond-length-within-tolerance? bond-length 0.960061691781605 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. No Spacegroup found for this PDB file 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 54 read successfully DEBUG:: there were 0 types with no dictionary created 17 bond restraints created 31 angle restraints created 0 plane restraints created 1 chiral vol restraints created 49 restraints INFO:: make_restraints(): made 67 non-bonded restraints initial distortion_score: 903.1 Initial RMS Z values bonds: 5.621 angles: 3.433 torsions: N/A planes: N/A non-bonded: 0 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: 0.009429 angles: 0.121 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1385 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 11.23 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Tue_Jan__2_23:43:56_2018_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)) created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 28 restraints INFO:: make_restraints(): made 39 non-bonded restraints initial distortion_score: 1506 Initial RMS Z values bonds: 1.152 angles: 0.8476 torsions: N/A planes: 3.056 non-bonded: 81.91 chiral vol: 0.7578 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 67) at -1706 Final Estimated RMS Z Scores: bonds: 0.7868 angles: 0.6326 torsions: N/A planes: 0.4938 non-bonded: 0.02131 chiral vol: 0.5393 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 11.28 Refinement elapsed time: 0.014 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:43:56_2018_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: 2.62176615612904: bond-length-within-tolerance? bond-length 2.62176615612904 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.3898696899414 4.69710969924927 19.6972827911377)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.6724548339844 6.87509822845459 19.0008640289307)) created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: make_restraints(): made 36 non-bonded restraints initial distortion_score: 837.6 Initial RMS Z values bonds: 14.58 angles: 0.6326 torsions: N/A planes: 0.4938 non-bonded: 0 chiral vol: 0.5393 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 86) at -1751 Final Estimated RMS Z Scores: bonds: 0.6693 angles: 0.6436 torsions: N/A planes: 1.145 non-bonded: 0 chiral vol: 0.5848 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 11.3 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:43:56_2018_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.51830724599225: bond-length-within-tolerance? bond-length 1.51830724599225 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5025482177734 4.84182024002075 19.5439510345459)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.2850494384766 6.0966649055481 19.1999835968018)) 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 56 read successfully DEBUG:: there were 1 types with no dictionary Welcome to Coot WARNING:: bond_restraint_length 4 should be 5 created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 15 restraints INFO:: make_restraints(): made 7 non-bonded restraints initial distortion_score: 4864 Initial RMS Z values bonds: 0.01199 angles: 0.00654 torsions: N/A planes: 0 non-bonded: 689.9 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 77) at -385.7 Final Estimated RMS Z Scores: bonds: 0.1585 angles: 0.04501 torsions: N/A planes: 0.07964 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 11.85 Refinement elapsed time: 0.014 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Tue_Jan__2_23:43:57_2018_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 57 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_2.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_3.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_6.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_7.pdb.gz INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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_Tue_Jan__2_23:43:57_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:57_2018_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 60 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_Tue_Jan__2_23:43:58_2018_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 61 read successfully DEBUG:: there were 0 types with no dictionary INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] 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 62 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 62 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -3 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 DEBUG:: s.length() 95 DEBUG:: nSelResidues 87 INFO:: backup file coot-backup/_home_paule_data_greg-data_rnase-A-needs-an-insertion.pdb_Tue_Jan__2_23:43:58_2018_modification_0.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 The alignment resulted in the following Insertions (coalesced): from 1 to 4 ASP VAL SER from 11 to 14 LEU PRO PRO from 62 to 64 PRO GLY Insertions (singles): [spec: 197480936 "A" 1 ""] -> ASP [spec: 197480936 "A" 2 ""] -> VAL [spec: 197480936 "A" 3 ""] -> SER [spec: 197480936 "A" 11 ""] -> LEU [spec: 197480936 "A" 12 ""] -> PRO [spec: 197480936 "A" 13 ""] -> PRO [spec: 197480936 "A" 62 ""] -> PRO [spec: 197480936 "A" 63 ""] -> GLY Deletions: [spec: 197480936 "A" 25 ""] [spec: 197480936 "A" 34 ""] Mutations: [spec: 197480936 "A" 24 ""] -> SER [spec: 197480936 "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 63 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:59_2018_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 64 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:43:59_2018_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3hfl.ent PDB file /home/paule/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file 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 65 read successfully DEBUG:: there were 1 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.017 seconds to read MTZ file INFO:: 0.006 seconds to initialize map INFO:: 0.012 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 7.462e-11 Map sigma: ....... 0.2604 Map maximum: ..... 1.718 Map minimum: ..... -1.034 INFO:: 0.006 seconds for contour map INFO:: 0.044 seconds in total INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Tue_Jan__2_23:44:00_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.834 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Tue_Jan__2_23:44:00_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.01207 rms devi: 0.01345 max devi: 0.02142 min devi: 0.003856 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08463 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: 0.335 max devi: 0.536 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: 0.01198 rms devi: 0.01335 max devi: 0.02126 min devi: 0.003873 INFO:: 5 matched atoms had: mean devi: 0.0002426 rms devi: 0.0002428 max devi: 0.0002567 min devi: 0.0002313 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08456 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: 6.931e-05 rms devi: 6.936e-05 max devi: 7.334e-05 min devi: 6.608e-05 INFO:: 5 matched atoms had: mean devi: 0.01203 rms devi: 0.01341 max devi: 0.02135 min devi: 0.003862 INFO:: 5 matched atoms had: mean devi: 0.0001386 rms devi: 0.0001387 max devi: 0.0001467 min devi: 0.0001322 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.01337 max devi: 0.02129 min devi: 0.003869 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: 0.08481 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_Tue_Jan__2_23:44:00_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Jan__2_23:44:00_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.3372 max devi: 0.5475 min devi: 0.08176 INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.01207 rms devi: 0.01345 max devi: 0.02142 min devi: 0.003856 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08463 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: 0.335 max devi: 0.536 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: 0.01198 rms devi: 0.01335 max devi: 0.02126 min devi: 0.003873 INFO:: 5 matched atoms had: mean devi: 0.0002426 rms devi: 0.0002428 max devi: 0.0002567 min devi: 0.0002313 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08456 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: 6.931e-05 rms devi: 6.936e-05 max devi: 7.334e-05 min devi: 6.608e-05 INFO:: 5 matched atoms had: mean devi: 0.01203 rms devi: 0.01341 max devi: 0.02135 min devi: 0.003862 INFO:: 5 matched atoms had: mean devi: 0.0001386 rms devi: 0.0001387 max devi: 0.0001467 min devi: 0.0001322 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.01337 max devi: 0.02129 min devi: 0.003869 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: 0.08481 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_Tue_Jan__2_23:44:00_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Jan__2_23:44:00_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.3372 max devi: 0.5475 min devi: 0.08176 INFO:: 5 matched atoms had: mean devi: 0.005899 rms devi: 0.00671 max devi: 0.01013 min devi: 0.002581 INFO:: 5 matched atoms had: mean devi: 0.007256 rms devi: 0.007788 max devi: 0.01256 min devi: 0.00456 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08783 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: 0.007179 rms devi: 0.0077 max devi: 0.01241 min devi: 0.004575 INFO:: 5 matched atoms had: mean devi: 0.005744 rms devi: 0.006571 max devi: 0.009959 min devi: 0.002425 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08776 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: 0.005854 rms devi: 0.006669 max devi: 0.01008 min devi: 0.002535 INFO:: 5 matched atoms had: mean devi: 0.007225 rms devi: 0.007753 max devi: 0.0125 min devi: 0.004565 INFO:: 5 matched atoms had: mean devi: 0.00581 rms devi: 0.006629 max devi: 0.01003 min devi: 0.00249 INFO:: 5 matched atoms had: mean devi: 0.007194 rms devi: 0.007718 max devi: 0.01244 min devi: 0.004572 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: 0.08801 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_Tue_Jan__2_23:44:00_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.09235 INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004329 rms devi: 0.004818 max devi: 0.007383 min devi: 0.001862 INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.326 max devi: 0.5019 min devi: 0.09266 INFO:: 5 matched atoms had: mean devi: 0.005899 rms devi: 0.00671 max devi: 0.01013 min devi: 0.002581 INFO:: 5 matched atoms had: mean devi: 0.007256 rms devi: 0.007788 max devi: 0.01256 min devi: 0.00456 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08783 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: 0.007179 rms devi: 0.0077 max devi: 0.01241 min devi: 0.004575 INFO:: 5 matched atoms had: mean devi: 0.005744 rms devi: 0.006571 max devi: 0.009959 min devi: 0.002425 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08776 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: 0.005854 rms devi: 0.006669 max devi: 0.01008 min devi: 0.002535 INFO:: 5 matched atoms had: mean devi: 0.007225 rms devi: 0.007753 max devi: 0.0125 min devi: 0.004565 INFO:: 5 matched atoms had: mean devi: 0.00581 rms devi: 0.006629 max devi: 0.01003 min devi: 0.00249 INFO:: 5 matched atoms had: mean devi: 0.007194 rms devi: 0.007718 max devi: 0.01244 min devi: 0.004572 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: 0.08801 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_Tue_Jan__2_23:44:00_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.09235 INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004329 rms devi: 0.004818 max devi: 0.007383 min devi: 0.001862 INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:00_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.326 max devi: 0.5019 min devi: 0.09266 INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:00_2018_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/some-waters-with-ter.pdb PDB file /home/paule/data/greg-data/some-waters-with-ter.pdb has been read. No Spacegroup found for this PDB file 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 72 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_Tue_Jan__2_23:44:00_2018_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 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 73 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 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3115 INFO:: Using density cut-off: 0.623 (2 sigma) (mean -0.03383 stdev: 0.1463) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4 3.2 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 59.89, 3.041, -4.33) is too big to be water INFO:: cluster at xyz = ( 70.01, 19.08, 18.6) is too big to be water INFO:: cluster at xyz = ( 52.98, 9.035, 20.15) is too big to be water INFO:: found 54 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_tm+some-waters.pdb_Tue_Jan__2_23:44:01_2018_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 74 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:01_2018_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 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. No Spacegroup found for this PDB file 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 75 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_Tue_Jan__2_23:44:04_2018_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /home/paule/data/greg-data/pathological-water-test.pdb PDB file /home/paule/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 76 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_pathological-water-test.pdb_Tue_Jan__2_23:44:04_2018_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.024 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.041e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.014 seconds for contour map INFO:: 0.058 seconds in total fitting terminal residue with 1000 random trials called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1 DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms DEBUG:: oops residue subject_res_num 92 - No atoms 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_Tue_Jan__2_23:44:04_2018_modification_0.pdb.gz INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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: 79 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 79 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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_Tue_Jan__2_23:44:05_2018_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 80 read successfully DEBUG:: there were 0 types with no dictionary 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.6,8.687,12.91) B-factor: 45 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.6,8.687,12.91) B-factor: 45 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.6,8.687,12.91) B-factor: 45 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.6,8.687,12.91) B-factor: 45 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.6,8.687,12.91) B-factor: 45 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.6,8.687,12.91) B-factor: 45 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.6,8.687,12.91) B-factor: 45 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.6,8.687,12.91) B-factor: 45 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.6,8.687,12.91) B-factor: 45 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.6,8.687,12.91) B-factor: 45 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.6,8.687,12.91) B-factor: 45 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.6,8.687,12.91) B-factor: 45 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.6,8.687,12.91) B-factor: 45 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.6,8.687,12.91) B-factor: 45 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 81 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 82 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 83 read successfully DEBUG:: there were 1 types with no dictionary -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0 0 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: (62.57,-20.5,95.47) B-factor: 45.26 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (64.42,-37.85,121.4) B-factor: 88.52 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.499 rms devi: 2.796 max devi: 6.686 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: (62.57,-20.5,95.47) B-factor: 45.26 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (-18.26,-63.04,111.4) B-factor: 50.76 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.971 rms devi: 2.173 max devi: 4.541 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: (62.57,-20.5,95.47) B-factor: 45.26 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (-0.2911,-72.48,94.47) B-factor: 78.35 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.704 rms devi: 4.086 max devi: 9.438 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 0/67 INFO:: NCS chain comparison 0/54 INFO:: NCS chain comparison 0/54 INFO:: NCS chain comparison 0/1 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:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 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:: Matching/moving molecule number 86 to 85 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.03532 rms devi: 0.03779 max devi: 0.05453 min devi: 0.01668 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_Tue_Jan__2_23:44:06_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) PASS: update monomer restraints Entered testcase - Write mmCIF restraints correctly PASS: Write mmCIF restraints correctly Entered testcase - Refinement OK with zero bond esd PASS: Refinement OK with zero bond esd Entered testcase - Change Chain IDs and Chain Sorting PASS: Change Chain IDs and Chain Sorting Entered testcase - 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 ::::: (62 "A" 1 "") #f #f ::::: (62 "A" 4 "") #t #t ::::: (62 "A" 57 "") #t #t ::::: (62 "A" 60 "") #f #f ::::: (62 "A" 61 "") #f #f ::::: (62 "A" 92 "") #t #t ::::: (62 "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 - 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 87 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 88 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 87 to 88 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.5023 rms devi: 0.5938 max devi: 1.679 min devi: 0.04318 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_Tue_Jan__2_23:44:07_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 89 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:08_2018_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 90 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 91 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 92 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.022 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.041e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.013 seconds for contour map INFO:: 0.055 seconds in total masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:09_2018_modification_0.pdb.gz INFO:: replace_coords: 745 atoms updated. SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.903 13.7 9.237 90 98.21 90 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 94 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.32 34.32 11.09 90 90 90 READ-INS:: Spacegroup: "I 41 2 2" INFO:: read_file() chain with chain id has 2 residues Symmetry available for this molecule Molecule 95 read successfully INFO:: spacegroup: I 41 2 2 LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.73 77.73 77.73 90 90 90 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 96 read successfully Map statistics: mean: -5.07e-05 st.d: 0.3052 Map statistics: min: -0.781, max: 6.079 -0.6953 231 -0.5238 4724 -0.3523 24910 -0.1808 55291 -0.00927 95241 0.1622 40930 0.3337 7480 0.5052 3968 0.6767 2790 0.8482 2117 1.02 1738 1.191 1221 1.363 888 1.534 595 1.706 355 1.877 240 2.049 137 2.22 97 2.392 62 2.563 46 2.735 17 2.906 17 3.078 13 3.249 10 3.421 7 3.592 1 3.764 3 3.935 7 4.107 2 4.278 5 4.45 1 4.621 2 4.793 2 4.964 0 5.136 1 5.307 0 5.479 0 5.65 0 5.822 0 5.993 0 6.165 1 Map statistics: mean: -1.005e-05 st.d: 0.04681 Map statistics: min: -0.2115, max: 0.6486 -0.2008 7 -0.1793 48 -0.1578 209 -0.1363 787 -0.1148 2257 -0.09325 5676 -0.07175 12730 -0.05025 24380 -0.02874 38191 -0.007239 46229 0.01427 43880 0.03577 32484 0.05727 19420 0.07878 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 ((90 "A" 1 "") (90 "A" 2 "") (90 "A" 3 "") (90 "A" 4 "") (90 "A" 5 "") (90 "A" 6 "") (90 "A" 7 "") (90 "A" 8 "") (90 "A" 9 "") (90 "A" 10 "") (90 "A" 11 "") (90 "A" 12 "") (90 "A" 13 "") (90 "A" 14 "") (90 "A" 15 "") (90 "A" 16 "") (90 "A" 17 "") (90 "A" 18 "") (90 "A" 19 "") (90 "A" 20 "") (90 "A" 21 "") (90 "A" 22 "") (90 "A" 23 "") (90 "A" 24 "") (90 "A" 25 "") (90 "A" 26 "") (90 "A" 27 "") (90 "A" 28 "") (90 "A" 29 "") (90 "A" 30 "") (90 "A" 31 "") (90 "A" 32 "") (90 "A" 33 "") (90 "A" 34 "") (90 "A" 35 "") (90 "A" 36 "") (90 "A" 37 "") (90 "A" 38 "") (90 "A" 39 "") (90 "A" 40 "") (90 "A" 41 "") (90 "A" 42 "") (90 "A" 43 "") (90 "A" 44 "") (90 "A" 45 "") (90 "A" 46 "") (90 "A" 47 "") (90 "A" 48 "") (90 "A" 49 "") (90 "A" 50 "") (90 "A" 51 "") (90 "A" 52 "") (90 "A" 53 "") (90 "A" 54 "") (90 "A" 55 "") (90 "A" 56 "") (90 "A" 57 "") (90 "A" 58 "") (90 "A" 59 "") (90 "A" 60 "") (90 "A" 61 "") (90 "A" 62 "") (90 "A" 63 "") (90 "A" 64 "") (90 "A" 65 "") (90 "A" 66 "") (90 "A" 67 "") (90 "A" 68 "") (90 "A" 69 "") (90 "A" 70 "") (90 "A" 71 "") (90 "A" 72 "") (90 "A" 73 "") (90 "A" 74 "") (90 "A" 75 "") (90 "A" 76 "") (90 "A" 77 "") (90 "A" 78 "") (90 "A" 79 "") (90 "A" 80 "") (90 "A" 81 "") (90 "A" 82 "") (90 "A" 83 "") (90 "A" 84 "") (90 "A" 85 "") (90 "A" 86 "") (90 "A" 87 "") (90 "A" 88 "") (90 "A" 89 "") (90 "A" 90 "") (90 "A" 91 "") (90 "A" 92 "") (90 "A" 93 "") (90 "B" 1 "") (90 "B" 2 "") (90 "B" 3 "") (90 "B" 4 "") (90 "B" 5 "") (90 "B" 6 "") (90 "B" 7 "") (90 "B" 8 "") (90 "B" 9 "") (90 "B" 10 "") (90 "B" 11 "") (90 "B" 12 "") (90 "B" 13 "") (90 "B" 14 "") (90 "B" 15 "") (90 "B" 16 "") (90 "B" 17 "") (90 "B" 18 "") (90 "B" 19 "") (90 "B" 20 "") (90 "B" 21 "") (90 "B" 22 "") (90 "B" 23 "") (90 "B" 24 "") (90 "B" 25 "") (90 "B" 26 "") (90 "B" 27 "") (90 "B" 28 "") (90 "B" 29 "") (90 "B" 30 "") (90 "B" 31 "") (90 "B" 32 "") (90 "B" 33 "") (90 "B" 34 "") (90 "B" 35 "") (90 "B" 36 "") (90 "B" 37 "") (90 "B" 38 "") (90 "B" 39 "") (90 "B" 40 "") (90 "B" 41 "") (90 "B" 42 "") (90 "B" 43 "") (90 "B" 44 "") (90 "B" 45 "") (90 "B" 46 "") (90 "B" 47 "") (90 "B" 48 "") (90 "B" 49 "") (90 "B" 50 "") (90 "B" 51 "") (90 "B" 52 "") (90 "B" 53 "") (90 "B" 54 "") (90 "B" 55 "") (90 "B" 56 "") (90 "B" 57 "") (90 "B" 58 "") (90 "B" 59 "") (90 "B" 60 "") (90 "B" 61 "") (90 "B" 62 "") (90 "B" 63 "") (90 "B" 64 "") (90 "B" 65 "") (90 "B" 66 "") (90 "B" 67 "") (90 "B" 68 "") (90 "B" 69 "") (90 "B" 70 "") (90 "B" 71 "") (90 "B" 72 "") (90 "B" 73 "") (90 "B" 74 "") (90 "B" 75 "") (90 "B" 76 "") (90 "B" 77 "") (90 "B" 78 "") (90 "B" 79 "") (90 "B" 80 "") (90 "B" 81 "") (90 "B" 82 "") (90 "B" 83 "") (90 "B" 84 "") (90 "B" 85 "") (90 "B" 86 "") (90 "B" 87 "") (90 "B" 88 "") (90 "B" 89 "") (90 "B" 90 "") (90 "B" 91 "") (90 "B" 92 "") (90 "B" 93 "") (90 "B" 94 "") (90 "B" 95 "") (90 "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 testcase - new molecule by atom selection inherits shelx molecule flag PASS: new molecule by atom selection inherits shelx molecule flag Entered testcase - Addition of Terminal Residue on SHELX mfitting terminal residue with 1000 random trials called fit_terminal_residue_generic() residue-seqnum: 2020 offset: 1 DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms DEBUG:: oops residue subject_res_num 2019 - No atoms 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_Tue_Jan__2_23:44:10_2018_modification_0.res WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CD2" INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Tue_Jan__2_23:44:10_2018_modification_0.res WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3052 INFO:: Using density cut-off: 0.1831 (0.6 sigma) (mean -0.02035 stdev: 0.1119) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4 3.2 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_Tue_Jan__2_23:44:10_2018_modification_1.res WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" INFO:: Adding to solvent chain: D LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.14 83.03 89.79 90 90 90 READ-INS:: Spacegroup: "P 21 21 21" INFO:: read_file() chain with chain id has 5 residues Symmetry available for this molecule Molecule 101 read successfully LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.7 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id has 23 residues Symmetry available for this molecule Molecule 102 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 14.08 32.76 18.66 90 101.7 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: read_file() chain with chain id A has 23 residues Symmetry available for this molecule Molecule 103 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 109 109 107.6 90 90 90 READ-INS:: Spacegroup: "I 4 2 2" INFO:: read_file() chain with chain id has 4 residues Symmetry available for this molecule Molecule 104 read successfully INFO:: Creating directory coot-ccp4 olecule has correct occupancy PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy Entered testcase - Add water to SHELX molecule PASS: Add water to SHELX molecule Entered testcase - Find Waters for a SHELXL molecule PASS: Find Waters for a SHELXL molecule Entered testcase - NPD Anisotropic Atom [Mitch Miller] PASS: NPD Anisotropic Atom [Mitch Miller] Entered testcase - close shelx molecules PASS: close shelx molecules Entered testcase - Aniso Bs in P21 b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) PASS: Aniso Bs in P21 Entered testcase - Don't crash on reading a strange HAT file PASS: Don't crash on reading a strange HAT file Ended 02-shelx.scm Running 03-ligand.scm ... Entered testcase - Get monomer test run-command-in-dir dir: "coot-ccp4/" exe: "libcheck" cl-args: () data-lines: ("N" "MON 3GP" "") log-file-name: "coot-libcheck-3GP.log" #t : : --- LIBCHECK --- /Vers 5.2.00 ; 12.12.2011/ : : : Do you want to have FILE-DOCUMENT /libcheck.doc/ ? //Y/A : : N - means without DOC-file : Y - with new contents : A - means to keep old contents and add new information : with DOC-file program creates batch file: libcheck.bat : _DOC: : : # : # Keywords: : # : #FILE_L: < > - additional library, " " means without this file : #MON: < > - give info about this monomer : # if = * , give list all monomers in the library : #FILE_PDB: < > - input PDB_file ," " means without this file : #FILE_SMILE: < > - input SMILE_file ," " means without this fil e : #FILE_SDF: < > - input SDF file, " " means without this file : #FILE_MOL: < > - input MOL (sybil), SDF, ODB (O) files : # use keyword MON as compound_id : #FILE_CIF: < > - input CIFile ," " means without this file : #FILE_CSD: < > - input CSD CIFile," " means without this file : #HFLAG: /A/N - Y - hydrogen atoms where they are : # A - with all hydrogen atoms : # N - without hydrogen atoms : #IND: /Y - Y - create index of mon_lib.cif : # output file: "new_mon_lib_ind.cif" : #FILE_O: - output files /library,coords,ps/, name without : # extention : #FILE_L2: < > - additional library (FILE_L) will be added to this library : # in this case program performs only adding : #ANGLE: <0.0> - rotation angle for picture ( around X ) : #LIST: /S/L - S short output, L - long, M - medium : #REF: /S,N,0 - 0 no refinement of new monomer : # N only crd->ang and ang->crd : # S plus torsion ref, Y plus restr.ref : # : #TEST: <0> - for program testing only : #COOR: /Y - use Vobs from coords instead Videal : #LCOOR: /N - Y use coords from lib description : #NODIST: /Y - Y not read the distributed library : # (only with FILE_L) : #SRCH: /Y/0 - Y - global search, 0 - for MON from PDB_file : # (only with NODIST = N) : : #--- type "keyword parameters" and/or --- : #--- press key "CR" to run program --- : --> --> MON : 3GP : ------------- : ------------- : Keywords: : HFLAG : Y : COOR : N : LCOOR : Y : SRCH : N : REF : Y : NODIST: N : NUMBER OF MONOMERS IN THE LIBRARY : 11459 : with complete description : 11459 : NUMBER OF MODIFICATIONS : 53 : NUMBER OF LINKS : 66 : I am reading libraries. Please wait. : - energy parameters : - monomer"s description (links & mod ) : I am reading library. Please wait. : - monomer"s description : * CIFile : libcheck_3GP.cif : * PDBfile : libcheck_3GP.pdb : * Plotfile: libcheck_3GP.ps : Output dictionary : mmcif : libcheck.lib : odb : libcheck.odb INFO:: libcheck status: 0 : : :
: : :
: 
: ###############################################################
: ###############################################################
: ###############################################################
: ### CCP4 6.3: Refmac_5.7.0029     version 5.7.0029 : 25/06/12##
: ###############################################################
: User: unknown  Run date:  2/ 1/2018 Run time: 23:44:12 
:
:
: Please reference: Collaborative Computational Project, Number 4. 1994.
: "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
: as well as any specific reference in the program write-up.
:
:
: $TEXT:Reference1: $$ Main reference $$ 
:   "REFMAC5 for the refinement of macromolecular crystal structures:"
:   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
:   Acta Crystallogr. D67, 355-367
:
: $$
: $SUMMARY :Reference1:  $$ Refmac: $$
: :TEXT:Reference1: $$
:
: $TEXT:Reference2: $$ Secondary reference $$ 
:   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
:   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
:   Acta Crystallogr. D53, 240-255
:   EU  Validation contract: BIO2CT-92-0524
:
: $$
: $SUMMARY :Reference2:  $$ Refmac: $$
: :TEXT:Reference2: $$
:
:  Data line--- MODE NEWENTRY
:  Data line--- END
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
:
:    ****                     Input and Default parameters#                      ****
:
:
:Input coordinate file.  Logical name - XYZIN actual file name  - coot-ccp4/libcheck_3GP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name - coot-ccp4/monomer-3GP.pdb
:
:  Refinement type                        : Idealisation
:
:
:    ****                           Makecif parameters                           ****
:
:Dictionary files for restraints : /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif
:User supplied dictionary entries: coot-ccp4/libcheck_3GP.cif
:    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
:    Hydrogens will be restored in their riding positions
:    hydrogens will be written to the output file
:    Links between monomers will be checked. Only those links present in the coordinate file will be used
:    Standard sugar links will be analysed and used
:    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
:    Symmetry related links will be analysed and used
:    Cis peptides will be found and used automatically
:
:
:
:
:Monitoring style is "MEDIUM". Complete information will be printed out in the
:first and last cycle. In all other cycles minimum information will be printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will be printed out
:Distance outliers      10.000
:Angle outliers         10.000
:Torsion outliers       10.000
:Chiral volume outliers 10.000
:Plane outliers         10.000
:Non-bonding outliers   10.000
:---------------------------------------------------------------
:
: Input file :coot-ccp4/libcheck_3GP.pdb
:  NUMBER OF MONOMERS IN THE LIBRARY          : 11459
:                with complete description    : 11459
:  NUMBER OF MODIFICATIONS                    :    53
:  NUMBER OF LINKS                            :    66
:  I am reading libraries. Please wait.
:      - energy parameters
:      - monomer"s description (links & mod )
:
:FORMATTED      OLD     file opened on unit  45
:
:Logical name: ATOMSF, Filename: /home/paule/ccp4/ccp4-6.3.0/lib/data/atomsf.lib
:
:
:
: Spacegroup information obtained from library file: 
: Logical Name: SYMINFO   Filename: /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/share/coot/syminfo.lib
:
:  WARNING: "SCALE" card is absent in input PDB file
:  Number of atoms    :      36
:  Number of residues :       1
:  Number of chains   :       1
:  I am reading library. Please wait.
:                mon_lib.cif
:  --------------------------------
:  --- title of input coord file ---
:
:  PDB_code:3GP
:  PDB_name:coords of 3GP from prog: libcheck
:  PDB_date:XX-XXX-XX
:  --------------------------------
:  Number of chains                  :       1
:  Total number of monomers          :       1
:  Number of atoms                   :      36
:  Number of missing atoms           :       0
:  Number of rebuilt atoms           :       0
:  Number of unknown atoms           :       0
:  Number of deleted atoms           :       0
:
:
: loop_
:     _atom_type_symbol
:     _atom_type_scat_Cromer_Mann_a1
:     _atom_type_scat_Cromer_Mann_b1
:     _atom_type_scat_Cromer_Mann_a2
:     _atom_type_scat_Cromer_Mann_b2
:     _atom_type_scat_Cromer_Mann_a3
:     _atom_type_scat_Cromer_Mann_b3
:     _atom_type_scat_Cromer_Mann_a4
:     _atom_type_scat_Cromer_Mann_b4
:     _atom_type_scat_Cromer_Mann_c
:
:
:  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
:  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
:  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
:  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
:  P      6.4345   1.9067   4.1791  27.1570   1.7800   0.5260   1.4908  68.1645   1.1149
:
:
: Number of distances         :           0
: Number of angles            :           0
: Number of torsions          :           0
: Number of planes            :           0
: Number of chirals           :           0
: Number of intervals         :           0
:--------------------------------------------------------------------------------
:---------------------------------------
:                        Standard  External       All
:                Bonds:        38         0        38
:               Angles:        66         0        66
:              Chirals:         4         0         4
:               Planes:         2         0         2
:             Torsions:        22         0        22
:---------------------------------------
:
:
:
:     CGMAT cycle number =      1
:
: function value    19446.416    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.030     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     4.292     3.000
:Bond angles  : others                            26     1.222     3.000
:Torsion angles, period  1. refined               15     3.618    15.000
:Torsion angles, period  1. others                 3     0.015    15.000
:Torsion angles, period  3. refined                4     5.039    15.000
:Chiral centres: refined atoms                     4     0.186     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.005     0.020
:VDW repulsions.others                             6     0.189     0.200
:VDW; torsion: refined_atoms                       7     0.281     0.200
:VDW; torsion.others                               4     0.224     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       19446.416       363.92786       19446.416    
:
:
:     CGMAT cycle number =      2
:
: function value    363.92786    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.081     0.020
:Bond distances: others                           12     0.013     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       363.92786       1259.5922       363.92786    
:
: fvalues    0.0000000       363.92786       483.19171       363.92786    
:
:
:     CGMAT cycle number =      3
:
: function value    343.50781    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.079     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       343.50781       293.11017       343.50781    
:
:
:     CGMAT cycle number =      4
:
: function value    293.11017    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.076     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Gamma decreased to   1.66446306E-02
:
:
: fvalues    0.0000000       293.11017       287.58200       293.11017    
:
:
:     CGMAT cycle number =      5
:
: function value    287.58200    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   1.66446306E-02
: Gamma decreased to   9.13148280E-03
:
:
: fvalues    0.0000000       287.58200       230.52641       287.58200    
:
:
:     CGMAT cycle number =      6
:
: function value    230.52641    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.13148280E-03
: Not converging with gamma equal   9.13148280E-03
: Trying gamma equal   4.66972217E-02
: Gamma decreased to   3.91840748E-02
:
:
: fvalues    0.0000000       230.52641       281.71072       230.52641    
:
: fvalues    0.0000000       230.52641       242.13728       230.52641    
:
:
:     CGMAT cycle number =      7
:
: function value    233.00272    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.91840748E-02
: Gamma decreased to   3.23539414E-02
:
:
: fvalues    0.0000000       233.00272       230.08240       233.00272    
:
:
:     CGMAT cycle number =      8
:
: function value    230.08240    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.23539414E-02
: Gamma decreased to   2.61447281E-02
:
:
: fvalues    0.0000000       230.08240       229.98131       230.08240    
:
:
:     CGMAT cycle number =      9
:
: function value    229.98131    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.61447281E-02
: Gamma decreased to   2.04999894E-02
:
:
: fvalues    0.0000000       229.98131       229.51228       229.98131    
:
:
:     CGMAT cycle number =     10
:
: function value    229.51228    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.04999894E-02
: Not converging with gamma equal   2.04999894E-02
: Trying gamma equal   4.87236828E-02
: Not converging with gamma equal   4.87236828E-02
: Trying gamma equal   7.97697455E-02
: Not converging with gamma equal   7.97697455E-02
: Trying gamma equal   0.11392042    
: Not converging with gamma equal   0.11392042    
: Trying gamma equal   0.15148616    
: Not converging with gamma equal   0.15148616    
: Trying gamma equal   0.19280848    
: Gamma decreased to   0.18454401    
:
:
: fvalues    0.0000000       229.51228       229.47993       229.51228    
:
:
:     CGMAT cycle number =     11
:
: function value    229.47993    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.18454401    
: Gamma decreased to   0.17703086    
:
:
: fvalues    0.0000000       229.47993       229.44974       229.47993    
:
:
:     CGMAT cycle number =     12
:
: function value    229.44974    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17703086    
: Gamma decreased to   0.17020072    
:
:
: fvalues    0.0000000       229.44974       229.42068       229.44974    
:
:
:     CGMAT cycle number =     13
:
: function value    229.42068    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17020072    
: Gamma decreased to   0.16399151    
:
:
: fvalues    0.0000000       229.42068       229.39333       229.42068    
:
:
:     CGMAT cycle number =     14
:
: function value    229.39333    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.16399151    
: Gamma decreased to   0.15834677    
:
:
: fvalues    0.0000000       229.39333       229.36681       229.39333    
:
:
:     CGMAT cycle number =     15
:
: function value    229.36681    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15834677    
: Gamma decreased to   0.15321518    
:
:
: fvalues    0.0000000       229.36681       229.34163       229.36681    
:
:
:     CGMAT cycle number =     16
:
: function value    229.34163    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15321518    
: Gamma decreased to   0.14855011    
:
:
: fvalues    0.0000000       229.34163       229.31769       229.34163    
:
:
:     CGMAT cycle number =     17
:
: function value    229.31769    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14855011    
: Gamma decreased to   0.14430913    
:
:
: fvalues    0.0000000       229.31769       229.29506       229.31769    
:
:
:     CGMAT cycle number =     18
:
: function value    229.29506    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14430913    
: Gamma decreased to   0.14045370    
:
:
: fvalues    0.0000000       229.29506       229.27348       229.29506    
:
:
:     CGMAT cycle number =     19
:
: function value    229.27348    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14045370    
: Gamma decreased to   0.13694876    
:
:
: fvalues    0.0000000       229.27348       229.25328       229.27348    
:
:
:     CGMAT cycle number =     20
:
: function value    229.25328    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13694876    
: Gamma decreased to   0.13376246    
:
:
: fvalues    0.0000000       229.25328       229.23459       229.25328    
:
:
:     CGMAT cycle number =      1
:
: function value    3954.6292    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     3.958     3.000
:Bond angles  : others                            26     1.410     3.000
:Torsion angles, period  1. refined               15     1.476    15.000
:Torsion angles, period  1. others                 3     0.190    15.000
:Torsion angles, period  3. refined                4     7.029    15.000
:Chiral centres: refined atoms                     4     0.035     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             1     0.000     0.200
:VDW; torsion: refined_atoms                       6     0.007     0.200
:VDW; torsion.others                               6     0.000     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       3954.6292       1645.5861       3954.6292    
:
:
:     CGMAT cycle number =      2
:
: function value    1645.5861    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.064     0.020
:Bond distances: others                           12     0.011     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       1645.5861       1504.8378       1645.5861    
:
:
:     CGMAT cycle number =      3
:
: function value    1504.8378    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.054     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       1504.8378       1416.2617       1504.8378    
:
:
:     CGMAT cycle number =      4
:
: function value    1416.2617    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.048     0.020
:Bond distances: others                           12     0.008     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Not converging with gamma equal   2.49090921E-02
: Trying gamma equal   7.03636408E-02
: Gamma decreased to   6.12727329E-02
:
:
: fvalues    0.0000000       1416.2617       1384.2695       1416.2617    
:
:
:     CGMAT cycle number =      5
:
: function value    1384.2695    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.045     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.12727329E-02
: Not converging with gamma equal   6.12727329E-02
: Trying gamma equal   0.10672728    
: Not converging with gamma equal   0.10672728    
: Trying gamma equal   0.15672728    
: Gamma decreased to   0.14672728    
:
:
: fvalues    0.0000000       1384.2695       1370.8711       1384.2695    
:
:
:     CGMAT cycle number =      6
:
: function value    1370.8711    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.045     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14672728    
: Gamma decreased to   0.13763636    
:
:
: fvalues    0.0000000       1370.8711       1358.0048       1370.8711    
:
:
:     CGMAT cycle number =      7
:
: function value    1358.0048    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.044     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13763636    
: Gamma decreased to   0.12937190    
:
:
: fvalues    0.0000000       1358.0048       1345.6464       1358.0048    
:
:
:     CGMAT cycle number =      8
:
: function value    1345.6464    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.043     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12937190    
: Gamma decreased to   0.12185875    
:
:
: fvalues    0.0000000       1345.6464       1333.7854       1345.6464    
:
:
:     CGMAT cycle number =      9
:
: function value    1333.7854    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.043     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12185875    
: Gamma decreased to   0.11502861    
:
:
: fvalues    0.0000000       1333.7854       1322.4045       1333.7854    
:
:
:     CGMAT cycle number =     10
:
: function value    1322.4045    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11502861    
: Gamma decreased to   0.10881940    
:
:
: fvalues    0.0000000       1322.4045       1311.4878       1322.4045    
:
:
:     CGMAT cycle number =     11
:
: function value    1311.4878    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10881940    
: Gamma decreased to   0.10317466    
:
:
: fvalues    0.0000000       1311.4878       1301.0240       1311.4878    
:
:
:     CGMAT cycle number =     12
:
: function value    1301.0240    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10317466    
: Gamma decreased to   9.80430841E-02
:
:
: fvalues    0.0000000       1301.0240       1290.9941       1301.0240    
:
:
:     CGMAT cycle number =     13
:
: function value    1290.9941    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.80430841E-02
: Not converging with gamma equal   9.80430841E-02
: Trying gamma equal   0.12370099    
: Gamma decreased to   0.11856941    
:
:
: fvalues    0.0000000       1290.9941       1283.1353       1290.9941    
:
:
:     CGMAT cycle number =     14
:
: function value    1283.1353    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11856941    
: Gamma decreased to   0.11390433    
:
:
: fvalues    0.0000000       1283.1353       1275.5366       1283.1353    
:
:
:     CGMAT cycle number =     15
:
: function value    1275.5366    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11390433    
: Gamma decreased to   0.10966336    
:
:
: fvalues    0.0000000       1275.5366       1268.1951       1275.5366    
:
:
:     CGMAT cycle number =     16
:
: function value    1268.1951    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10966336    
: Gamma decreased to   0.10580793    
:
:
: fvalues    0.0000000       1268.1951       1261.1099       1268.1951    
:
:
:     CGMAT cycle number =     17
:
: function value    1261.1099    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10580793    
: Gamma decreased to   0.10230299    
:
:
: fvalues    0.0000000       1261.1099       1254.2709       1261.1099    
:
:
:     CGMAT cycle number =     18
:
: function value    1254.2709    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10230299    
: Gamma decreased to   9.91166830E-02
:
:
: fvalues    0.0000000       1254.2709       1247.6791       1254.2709    
:
:
:     CGMAT cycle number =     19
:
: function value    1247.6791    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.91166830E-02
: Gamma decreased to   9.62200388E-02
:
:
: fvalues    0.0000000       1247.6791       1241.3260       1247.6791    
:
:
:     CGMAT cycle number =     20
:
: function value    1241.3260    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.62200388E-02
: Gamma decreased to   9.35867280E-02
:
:
: fvalues    0.0000000       1241.3260       1235.2091       1241.3260    
:
:
:     CGMAT cycle number =      1
:
: function value    74.495377    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:Bond angles  : refined atoms                     40     2.272     3.000
:Bond angles  : others                            26     0.421     3.000
:Torsion angles, period  1. refined               15     5.524    15.000
:Torsion angles, period  1. others                 3    15.708    15.000
:Torsion angles, period  3. refined                4    13.494    15.000
:Chiral centres: refined atoms                     4     0.106     0.200
:Planar groups: refined atoms                     14     0.010     0.020
:Planar groups: others                             6     0.001     0.020
:VDW repulsions.others                             4     0.054     0.200
:VDW; torsion: refined_atoms                       4     0.320     0.200
:VDW; torsion.others                               6     0.092     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       74.495377       28.820347       74.495377    
:
:
:     CGMAT cycle number =      2
:
: function value    28.820347    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.009     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       28.820347       26.893410       28.820347    
:
:
:     CGMAT cycle number =      3
:
: function value    26.893410    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       26.893410       26.455139       26.893410    
:
:
:     CGMAT cycle number =      4
:
: function value    26.455139    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Not converging with gamma equal   2.49090921E-02
: Trying gamma equal   7.03636408E-02
: Gamma decreased to   6.12727329E-02
:
:
: fvalues    0.0000000       26.455139       26.371088       26.455139    
:
:
:     CGMAT cycle number =      5
:
: function value    26.371088    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.12727329E-02
: Not converging with gamma equal   6.12727329E-02
: Trying gamma equal   0.10672728    
: Not converging with gamma equal   0.10672728    
: Trying gamma equal   0.15672728    
: Not converging with gamma equal   0.15672728    
: Trying gamma equal   0.21172729    
: Gamma decreased to   0.20072728    
:
:
: fvalues    0.0000000       26.371088       26.350555       26.371088    
:
:
:     CGMAT cycle number =      6
:
: function value    26.350555    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.20072728    
: Gamma decreased to   0.19072728    
:
:
: fvalues    0.0000000       26.350555       26.334232       26.350555    
:
:
:     CGMAT cycle number =      7
:
: function value    26.334232    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.19072728    
: Gamma decreased to   0.18163636    
:
:
: fvalues    0.0000000       26.334232       26.320751       26.334232    
:
:
:     CGMAT cycle number =      8
:
: function value    26.320751    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.18163636    
: Gamma decreased to   0.17337190    
:
:
: fvalues    0.0000000       26.320751       26.309345       26.320751    
:
:
:     CGMAT cycle number =      9
:
: function value    26.309345    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17337190    
: Gamma decreased to   0.16585875    
:
:
: fvalues    0.0000000       26.309345       26.299595       26.309345    
:
:
:     CGMAT cycle number =     10
:
: function value    26.299595    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.16585875    
: Gamma decreased to   0.15902860    
:
:
: fvalues    0.0000000       26.299595       26.291113       26.299595    
:
:
:     CGMAT cycle number =     11
:
: function value    26.291113    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15902860    
: Gamma decreased to   0.15281940    
:
:
: fvalues    0.0000000       26.291113       26.283710       26.291113    
:
:
:     CGMAT cycle number =     12
:
: function value    26.283710    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15281940    
: Gamma decreased to   0.14717466    
:
:
: fvalues    0.0000000       26.283710       26.277178       26.283710    
:
:
:     CGMAT cycle number =     13
:
: function value    26.277178    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14717466    
: Gamma decreased to   0.14204307    
:
:
: fvalues    0.0000000       26.277178       26.271406       26.277178    
:
:
:     CGMAT cycle number =     14
:
: function value    26.271406    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14204307    
: Gamma decreased to   0.13737799    
:
:
: fvalues    0.0000000       26.271406       26.266275       26.271406    
:
:
:     CGMAT cycle number =     15
:
: function value    26.266275    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13737799    
: Gamma decreased to   0.13313702    
:
:
: fvalues    0.0000000       26.266275       26.261736       26.266275    
:
:
:     CGMAT cycle number =     16
:
: function value    26.261736    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13313702    
: Gamma decreased to   0.12928158    
:
:
: fvalues    0.0000000       26.261736       26.257744       26.261736    
:
:
:     CGMAT cycle number =     17
:
: function value    26.257744    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12928158    
: Gamma decreased to   0.12577665    
:
:
: fvalues    0.0000000       26.257744       26.254160       26.257744    
:
:
:     CGMAT cycle number =     18
:
: function value    26.254160    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12577665    
: Gamma decreased to   0.12259034    
:
:
: fvalues    0.0000000       26.254160       26.250973       26.254160    
:
:
:     CGMAT cycle number =     19
:
: function value    26.250973    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12259034    
: Gamma decreased to   0.11969370    
:
:
: fvalues    0.0000000       26.250973       26.248142       26.250973    
:
:
:     CGMAT cycle number =     20
:
: function value    26.248142    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11969370    
: Gamma decreased to   0.11706039    
:
:
: fvalues    0.0000000       26.248142       26.245613       26.248142    
:  Time in seconds: CPU =         0.42
:             Elapsed =           0.00
:
:    ****           Things for loggraph, R factor and others vs cycle            ****
:
:
:$TABLE: Rfactor analysis, stats vs cycle  :
:$GRAPHS: vs cycle :N:1,2,3:
::FOM vs cycle :N:1,4:
::-LL vs cycle :N:1,5:
::-LLfree vs cycle :N:1,6:
::Geometry vs cycle:N:1,7,8,9,10,11:
:$$
:    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
:$$
:       0   0.0      0.0      0.0           0.       0.0   0.0304  1.521   4.292  1.431   0.186
:       1   0.0      0.0      0.0           0.       0.0   0.0813  4.066   4.676  1.559   0.043
:       2   0.0      0.0      0.0           0.       0.0   0.0794  3.972   4.318  1.439   0.037
:       3   0.0      0.0      0.0           0.       0.0   0.0760  3.798   4.058  1.353   0.017
:       4   0.0      0.0      0.0           0.       0.0   0.0754  3.772   4.010  1.337   0.026
:       5   0.0      0.0      0.0           0.       0.0   0.0754  3.772   3.985  1.328   0.037
:       6   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.981  1.327   0.036
:       7   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.978  1.326   0.036
:       8   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.969  1.323   0.035
:       9   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.965  1.322   0.035
:      10   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      11   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      12   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      13   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      14   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.962  1.321   0.035
:      15   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      16   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      17   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      18   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      19   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.959  1.320   0.035
:      20   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.958  1.319   0.035
:      21   0.0      0.0      0.0           0.       0.0   0.0637  3.184   2.578  0.859   0.088
:      22   0.0      0.0      0.0           0.       0.0   0.0539  2.697   2.487  0.829   0.085
:      23   0.0      0.0      0.0           0.       0.0   0.0477  2.384   2.425  0.808   0.093
:      24   0.0      0.0      0.0           0.       0.0   0.0455  2.273   2.401  0.800   0.098
:      25   0.0      0.0      0.0           0.       0.0   0.0446  2.229   2.391  0.797   0.100
:      26   0.0      0.0      0.0           0.       0.0   0.0438  2.191   2.380  0.793   0.101
:      27   0.0      0.0      0.0           0.       0.0   0.0432  2.158   2.370  0.790   0.102
:      28   0.0      0.0      0.0           0.       0.0   0.0426  2.128   2.360  0.787   0.103
:      29   0.0      0.0      0.0           0.       0.0   0.0420  2.102   2.351  0.784   0.104
:      30   0.0      0.0      0.0           0.       0.0   0.0416  2.079   2.341  0.780   0.105
:      31   0.0      0.0      0.0           0.       0.0   0.0412  2.058   2.332  0.777   0.106
:      32   0.0      0.0      0.0           0.       0.0   0.0408  2.040   2.323  0.774   0.106
:      33   0.0      0.0      0.0           0.       0.0   0.0405  2.026   2.316  0.772   0.107
:      34   0.0      0.0      0.0           0.       0.0   0.0403  2.013   2.309  0.770   0.107
:      35   0.0      0.0      0.0           0.       0.0   0.0400  2.000   2.302  0.767   0.107
:      36   0.0      0.0      0.0           0.       0.0   0.0398  1.989   2.296  0.765   0.107
:      37   0.0      0.0      0.0           0.       0.0   0.0396  1.978   2.290  0.763   0.107
:      38   0.0      0.0      0.0           0.       0.0   0.0394  1.968   2.283  0.761   0.107
:      39   0.0      0.0      0.0           0.       0.0   0.0392  1.958   2.277  0.759   0.106
:      40   0.0      0.0      0.0           0.       0.0   0.0390  1.949   2.272  0.757   0.106
:      41   0.0      0.0      0.0           0.       0.0   0.0087  0.435   2.793  0.931   0.046
:      42   0.0      0.0      0.0           0.       0.0   0.0070  0.349   2.801  0.934   0.036
:      43   0.0      0.0      0.0           0.       0.0   0.0065  0.327   2.808  0.936   0.034
:      44   0.0      0.0      0.0           0.       0.0   0.0065  0.324   2.810  0.937   0.034
:      45   0.0      0.0      0.0           0.       0.0   0.0065  0.323   2.810  0.937   0.034
:      46   0.0      0.0      0.0           0.       0.0   0.0064  0.322   2.810  0.937   0.034
:      47   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.810  0.937   0.034
:      48   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.810  0.937   0.034
:      49   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.809  0.936   0.034
:      50   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.809  0.936   0.034
:      51   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      52   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      53   0.0      0.0      0.0           0INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 105 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:44:15_2018_modification_0.pdb.gz
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:44:15_2018_modification_1.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb
 PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 106 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Tue_Jan__2_23:44:16_2018_modification_0.pdb.gz
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb
 PDB file /home/paule/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
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 107 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.
No Spacegroup found for this PDB file
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 108 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:44:15_2018_modification_2.pdb.gz
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb
 PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 109 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 115 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.147 seconds to read MTZ file
INFO:: 0.095 seconds to initialize map
INFO:: 0.073 seconds for FFT
INFO:: 0.013 seconds for statistics
      Map mean: ........ -8.79e-07
      Map sigma: ....... 0.1712
      Map maximum: ..... 1.343
      Map minimum: ..... -0.6954
INFO:: 0.006 seconds for contour map
INFO:: 0.334 seconds in total
INFO:: making difference map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.072 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.072 seconds for FFT
INFO:: 0.014 seconds for statistics
      Map mean: ........ 2.094e-06
      Map sigma: ....... 0.03339
      Map maximum: ..... 0.3661
      Map minimum: ..... -0.1917
INFO:: 0.002 seconds for contour map
INFO:: 0.161 seconds in total
INFO:: ligand number 0 is molecule number 109   with wiggly flag: 0
in execute_ligand_search_internal() import maps from mol 116
INFO:: Protein centre at: xyz = (     58.29,     34.65,     30.63)
Map statistics: mean: -0.02167 st.d: 0.08863
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
  -0.09746    58214
  -0.06122    102889
  -0.02498    142998
   0.01126    471776
    0.0475    106846
   0.08375    56087
      0.12    21597
    0.1562    6911
    0.1925    2135
    0.2287    920
     0.265    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 sigma)  (mean -0.02168 stdev: 0.08862)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
debug:: n_ligands_for_cluster() top_score 4.042 and 4 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.018 and 8 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.09 and 4 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.859 and 6 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.391 and 10 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.684 and 8 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.096 and 8 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.636 and 8 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.07 and 3 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.857 and 5 are decent out of 12
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 129 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:44:27_2018_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:44:27_2018_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:44:27_2018_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:44:27_2018_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/dipole-residues.pdb
 PDB file /home/paule/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
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 131 read successfully
DEBUG:: there were 0 types with no dictionary 
WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
 PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 132 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 132
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 132
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 133 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.024 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.017 seconds for FFT
INFO:: 0.002 seconds for statistics
      Map mean: ........ 1.041e-09
      Map sigma: ....... 0.3115
      Map maximum: ..... 2.978
      Map minimum: ..... -0.875
INFO:: 0.012 seconds for contour map
INFO:: 0.055 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 133

Sequence: ?EYTVITPGARTR
Confidence: 1

From    : HEYTVITPGARTR
Chain id: 0	Offset: 53
INFO:: backup file coot-backup/_home_paule_data_greg-data_crashes_on_cootaneering-v2.pdb_Tue_Jan__2_23:44:30_2018_modification_0.pdb.gz
bypassing ? at 0
Mutating to GLU at 1
Mutating poly_ala residue number 58
Mutating to TYR at 2
Mutating poly_ala residue number 59
Mutating to THR at 3
Mutating poly_ala residue number 60
Mutating to VAL at 4
Mutating poly_ala residue number 61
Mutating to ILE at 5
Mutating poly_ala residue number 62
Mutating to THR at 6
Mutating poly_ala residue number 63
Mutating to PRO at 7
Mutating poly_ala residue number 64
Mutating to GLY at 8
Mutating poly_ala residue number 65
Mutating to ALA at 9
Mutating poly_ala residue number 66
Mutating to ARG at 10
Mutating poly_ala residue number 67
Mutating to THR at 11
Mutating poly_ala residue number 68
Mutating to ARG at 12
Mutating poly_ala residue number 69
DEBUG:: Creating a new chain B
WARNING:: no rotamers probabilities for residue type GLY
INFO:: replace_coords: 9 atoms updated.
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
INFO:: replace_coords: 12 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 8 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
WARNING:: no rotamers probabilities for residue type GLY
WARNING:: no rotamers probabilities for residue type ALA
INFO:: replace_coords: 11 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 11 atoms updated.
INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.01207
    rms devi: 0.01345
    max devi: 0.02142
    min devi: 0.003856
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.08463
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: 0.335
    max devi: 0.536
    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: 0.01198
    rms devi: 0.01335
    max devi: 0.02126
    min devi: 0.003873
INFO:: 5 matched atoms had: 
   mean devi: 0.0002426
    rms devi: 0.0002428
    max devi: 0.0002567
    min devi: 0.0002313
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.08456
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: 6.931e-05
    rms devi: 6.936e-05
    max devi: 7.334e-05
    min devi: 6.608e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.01203
    rms devi: 0.01341
    max devi: 0.02135
    min devi: 0.003862
INFO:: 5 matched atoms had: 
   mean devi: 0.0001386
    rms devi: 0.0001387
    max devi: 0.0001467
    min devi: 0.0001322
INFO:: 5 matched atoms had: 
   mean devi: 0.012
    rms devi: 0.01337
    max devi: 0.02129
    min devi: 0.003869
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: 0.08481
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_Tue_Jan__2_23:44:30_2018_modification_0.pdb.gz
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 0/8
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 0/8
INFO:: NCS chain comparison 8/8
First atom of 170 in first  selection 1/A/1 {G}/ P   altLoc :: segid :: pos: (67.8,-2.641,8.312) B-factor: 76.88
First atom of 170 in second selection 1/C/1 {G}/ P   altLoc :: segid :: pos: (91.77,21.39,32.47) B-factor: 76.88
INFO:: LSQ matched 8 atoms
INFO:: 8 matched atoms had: 
   mean devi: 0.1366
    rms devi: 0.1488
    max devi: 0.2364
    min devi: 0.06837
   find_ncs_matrix returns (LSQ) 
|         1, -0.001328, -0.001388|
|  0.001328,         1, 7.875e-05|
|  0.001388, -8.06e-05,         1|
(     -23.9,    -24.18,     -24.2)
INFO:: NCS chain comparison 0/8
INFO:: NCS chain comparison 0/8
INFO:: NCS chain comparison 8/8
First atom of 170 in first  selection 1/B/1 {C}/ P   altLoc :: segid :: pos: (69.19,-2.009,20.54) B-factor: 76.88
First atom of 170 in second selection 1/D/1 {C}/ P   altLoc :: segid :: pos: (93.32,22.21,44.71) B-factor: 76.88
INFO:: LSQ matched 8 atoms
INFO:: 8 matched atoms had: 
   mean devi: 0.09238
    rms devi: 0.09866
    max devi: 0.1642
    min devi: 0.05783
   find_ncs_matrix returns (LSQ) 
|         1,   0.00312,-0.0003107|
| -0.003121,         1, -0.005678|
|  0.000293,  0.005679,         1|
(     -24.2,    -23.62,    -24.33)
  INFO:: fill_ghost_info Constructed 2 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain A"
      Ghost 1 name: "NCS found from matching Chain D onto Chain B"
INFO:: Matching/moving molecule number 137 to 137
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: 0.02832
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_Tue_Jan__2_23:44:31_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|         1,  0.003218, -0.003497|
| -0.003225,         1, -0.001985|
|  0.003491,  0.001997,         1|
(    -24.05,     -23.7,    -24.44)
No unit cell for this molecule, hence no fractional matrix.
INFO:: Reading coordinate file: /home/paule/data/greg-data/1wly.pdb
 PDB file /home/paule/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
Molecule 138 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 139 read successfully
DEBUG:: there were 2 types with no dictionary 
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: reference 138 has 750 atoms selected
INFO:: moving    139 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_Tue_Jan__2_23:44:31_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|   -0.9117,   -0.3803,    0.1557|
|   -0.3625,    0.9227,     0.131|
|   -0.1935,   0.06299,   -0.9791|
(     70.65,     7.793,     21.29)
  Rotation - polar (omega,phi,kappa)  87.1413 101.0220 169.7385
  Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277
  Translation - Angstroms             70.6538 7.7930 21.2852 
INFO: core rmsd achieved: 1.0199 Angstroems
      number of residues in reference structure: 322
      number of residues in moving structure:    324
      number of residues in aligned sections (reference):  100
      number of residues in aligned sections (moving):     110
      number of aligned residues:  95
      number of gaps:              4
      number of misdirections:     0
      number of SSE combinations:  4.0000
      sequence identity:           30.5263%
WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb
.       0.0   0.0064  0.320   2.808  0.936   0.034
:      54   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      55   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      56   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      57   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
:      58   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
:      59   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:
: Refmac_5.7.0029:  End of Refmac_5.7.0029 
:Times: User:       2.5s System:    0.3s Elapsed:     0:03  
:
: : INFO:: libcheck-minimal? is #f PASS: Get monomer test Entered testcase - Set Bond thickness PASS: Set Bond thickness Entered testcase - Delete all-molecule Hydrogens here 1 PASS: Delete all-molecule Hydrogens Entered testcase - Non-Autoloads PASS: Non-Autoloads Entered testcase - Move and Refine Ligand test PASS: Move and Refine Ligand test Entered testcase - Many Molecules - Ligand Fitting Fitting NPO gave these results: # PASS: Many Molecules - Ligand Fitting Entered testcase - flip residue (around eigen vectors) distance: 4.35071918939919 distance d2: 1.19209289550781e-7 PASS: flip residue (around eigen vectors) Entered testcase - Test dipole info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0) PASS: Test dipole Entered testcase - Reading new dictionary restraints replaces PASS: Reading new dictionary restraints replaces 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 133 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/rnasa-1.8-all_refmac1.mtz FWT PHWT" 4 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 5 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 6 "test-3hfl.map" 7 "/home/paule/data/greg-data/tutorial-modern.pdb" 8 "mainchain" 9 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 10 "atom selection from tutorial-add-terminal-1-test.pdb" 11 "/home/paule/data/greg-data/frag-2wot.pdb" 12 "sphere selection from tutorial-modern.pdb" 14 "/home/paule/data/greg-data/rotamer-test-fragment.pdb" 15 "/home/paule/data/greg-data/res098.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 "/home/paule/data/greg-data/pdb3knw.ent" 19 "/home/paule/data/greg-data/pdb1py3.ent" 22 "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb" 23 "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 24 "/home/paule/data/greg-data/tutorial-modern.pdb" 25 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 26 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 27 "/home/paule/data/greg-data/tutorial-modern.pdb" 28 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 29 "/home/paule/data/greg-data/alt-conf-waters.pdb" 30 "/home/paule/data/greg-data/backrub-fragment.pdb" 31 "Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb" 32 "/home/paule/data/greg-data/coords-B3A.pdb" 33 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 34 "/home/paule/data/greg-data/test-TER-OXT.pdb" 35 "/home/paule/data/greg-data/val.pdb" 36 "/home/paule/data/greg-data/2yie-frag.pdb" 37 "/home/paule/data/greg-data/4f8g.pdb" 38 "/home/paule/data/greg-data/4f8g.pdb" 39 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 40 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 41 "/home/paule/data/greg-data/tutorial-modern.pdb" 42 "Generic Masked Map" 43 "difference-map" 46 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 47 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 48 "averaged-map" 49 "difference-map" 50 "/home/paule/data/greg-data/multi-carbo-coot-3.pdb" 51 "/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb" 52 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 53 "/home/paule/data/greg-data/monomer-VAL.pdb" 54 "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 55 "atom selection from tutorial-modern.pdb" 56 "/home/paule/data/greg-data/monomer-ACT.pdb" 57 "/home/paule/data/greg-data/tutorial-modern.pdb" 58 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 59 "atom selection from tutorial-modern.pdb" 60 "/home/paule/data/greg-data/tutorial-modern.pdb" 61 "/home/paule/data/greg-data/tutorial-modern.pdb" 62 "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb" 63 "/home/paule/data/greg-data/tutorial-modern.pdb" 64 "/home/paule/data/greg-data/tutorial-modern.pdb" 65 "/home/paule/data/greg-data/pdb3hfl.ent" 66 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 67 "Ideal-A-form-RNA" 68 "Ideal-A-form-RNA" 69 "Ideal-A-form-DNA" 70 "Ideal-A-form-DNA" 71 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 72 "/home/paule/data/greg-data/some-waters-with-ter.pdb" 73 "/home/paule/data/greg-data/tm+some-waters.pdb" 74 "/home/paule/data/greg-data/tutorial-modern.pdb" 75 "/home/paule/data/greg-data/water-test-no-cell.pdb" 76 "/home/paule/data/greg-data/pathological-water-test.pdb" 77 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 78 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 79 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 80 "/home/paule/data/greg-data/tutorial-modern.pdb" 81 "/home/paule/data/greg-data/pdb1hvv.ent" 82 "/home/paule/data/greg-data/monomer-ACT.pdb" 83 "/home/paule/data/greg-data/monomer-NPO.pdb" 84 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_81" 85 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 86 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 87 "/home/paule/data/greg-data/tutorial-modern.pdb" 88 "/home/paule/data/greg-data/pdb1py3.ent" 89 "/home/paule/data/greg-data/tutorial-modern.pdb" 90 "/home/paule/data/greg-data/tutorial-modern.pdb" 91 "/home/paule/data/greg-data/2goz-manip.pdb" 92 "/home/paule/data/greg-data/tutorial-modern.pdb" 93 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 94 "/home/paule/data/greg-data/HOF.RES" 95 "/home/paule/data/greg-data/hollander.ins" 98 "/home/paule/data/greg-data/insulin.fcf Diff-SigmaA" 99 "atom selection from insulin.res" 100 "atom selection from insulin.res" 102 "/home/paule/data/greg-data/horma-p21.res" 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 140 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 141 read successfully DEBUG:: there were 1 types with no dictionary INFO:: reference 140 has 169 atoms selected INFO:: moving 141 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_Tue_Jan__2_23:44:33_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491 Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832 Translation - Angstroms 0.3207 0.6598 0.8819 INFO: core rmsd achieved: 0.2210 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1.0000 sequence identity: 100.0000% LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 142 read successfully INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0230 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0170 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:: 0.0120 seconds for contour map INFO:: 0.0550 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 3 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 409600 out of 409600 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0006 st.d: 0.3256 Map statistics: min: -1.4696, max: 2.2923 -1.4225 2 -1.3285 5 -1.2344 5 -1.1404 10 -1.0463 9 -0.9523 37 -0.8583 141 -0.7642 493 -0.6702 1554 -0.5761 4667 -0.4821 12350 -0.3880 26465 -0.2940 43650 -0.1999 55555 -0.1059 57553 -0.0118 50690 0.0822 40145 0.1763 30074 0.2703 23268 0.3644 17859 0.4584 13062 0.5524 9524 0.6465 7028 0.7405 4917 0.8346 3611 0.9286 2439 1.0227 1610 1.1167 1087 1.2108 736 1.3048 442 1.3989 252 1.4929 160 1.5870 83 1.6810 49 1.7751 24 1.8691 17 1.9631 13 2.0572 4 2.1512 5 2.2453 5 2.3393 0 INFO:: installing ghost map with name :Map 143 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 148 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:34_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:34_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:34_2018_modification_2.pdb.gz INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 148 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 148 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_Tue_Jan__2_23:44:34_2018_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:34_2018_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 148 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 148 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_Tue_Jan__2_23:44:34_2018_modification_5.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1t6q.ent PDB file /home/paule/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 149 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_Tue_Jan__2_23:44:35_2018_modification_0.pdb.gz INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 149 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 149 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_Tue_Jan__2_23:44:35_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Tue_Jan__2_23:44:35_2018_modification_2.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 150 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 150 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:: 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:: Matching/moving molecule number 151 to 150 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_Tue_Jan__2_23:44:37_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) INFO:: 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:: Matching/moving molecule number 152 to 150 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_Tue_Jan__2_23:44:37_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.6203, -0.2279, -0.7505| | -0.4559, -0.6739, 0.5814| | -0.6382, 0.7028, 0.3141| ( -22.14, -19.93, 1.626) INFO:: fractional coordinates matrix: | -0.8835, -0.09252, -0.543| | -0.5264, -0.4107, 0.8789| | -0.4875, 0.7087, 0.3141| ( -0.381, -0.2605, 0.01406) INFO:: 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:: Matching/moving molecule number 153 to 150 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_Tue_Jan__2_23:44:37_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 154 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/1hvv_sigmaa.mtz Number of OBSERVED reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.0450 seconds to read MTZ file INFO:: 0.0210 seconds to initialize map INFO:: 0.0280 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:: 0.0060 seconds for contour map INFO:: 0.1040 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 155 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 155 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 155 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 155 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 155 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 155 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 155 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 155 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 155 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 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 164 read successfully DEBUG:: there were 0 types with no dictionary Entering test: OXT in restraints? INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NA.cif There are 2 data in /home/paule/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.1414 PASS: test symm trans to origin Entering test: test lsq plane LSQ deviations: 0.0000 0.0000 PASS: test lsq plane Entering test: test COO modification INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NA.cif INFO:: Reading coordinate file: /home/paule/data/greg-data/hideous-OXT.pdb PDB file /home/paule/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom created 7 bond restraints created 8 angle restraints created 1 plane restraints created 1 chiral vol restraints created 2 torsion restraints created 23 restraints INFO:: make_restraints(): made 13 non-bonded restraints initial distortion_score: 1241.5407 Initial RMS Z values bonds: 3.7208 angles: 7.4688 torsions: 0.2764 planes: 16.9011 non-bonded: 0.0000 chiral vol: 1.2266 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 243) at 0.0349 Final Estimated RMS Z Scores: bonds: 0.0017 angles: 0.0239 torsions: 0.1205 planes: 0.0019 non-bonded: 0.0000 chiral vol: 0.0068 rama plot: N/A start_pos: N/A GemanMcCl: N/A refinement_took 0.0060 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 103 "new-horma.ins" 104 "/home/paule/data/greg-data/crash.hat" 105 "coot-ccp4/monomer-3GP.pdb" 106 "/home/paule/data/greg-data/monomer-3GP.pdb" 107 "/home/paule/data/greg-data/test-LIG.pdb" 108 "/home/paule/data/greg-data/test-LIG.pdb" 109 "/home/paule/data/greg-data/monomer-NPO.pdb" 110 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 111 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 112 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 113 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 114 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 115 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 116 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 117 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 118 "Masked (by protein)" 119 "Fitted ligand #0-0" 120 "Fitted ligand #1-0" 121 "Fitted ligand #2-0" 122 "Fitted ligand #3-0" 123 "Fitted ligand #4-0" 124 "Fitted ligand #5-0" 125 "Fitted ligand #6-0" 126 "Fitted ligand #7-0" 127 "Fitted ligand #8-0" 128 "Fitted ligand #9-0" 129 "coot-ccp4/monomer-3GP.pdb" 130 "Copy_of_coot-ccp4/monomer-3GP.pdb" 131 "/home/paule/data/greg-data/dipole-residues.pdb" 132 "/home/paule/data/greg-data/tutorial-modern.pdb" 133 "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb" 134 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 135 "Ideal-A-form-RNA" 138 "/home/paule/data/greg-data/1wly.pdb" 139 "/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 155 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 155 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 155 NCS found from matching Chain D onto Chain A" n-matchers: 2 PASS: NCS maps overwrite existing maps Ended 07-ncs.scm Running 08-utils.scm ... Entered testcase - Test key symbols WARNING:: could not find key-sym-code for "missing key" PASS: Test key symbols Entered testcase - Test running a Python function test_val_2 passed test_val_3 passed PASS: Test running a Python function Entered testcase - Internal/External Molecule Numbers match PASS: Internal/External Molecule Numbers match Entered testcase - spacegroup operators to space group conversion PASS: spacegroup operators to space group conversion Ended 08-utils.scm Running 09-internal.scm ... Entered testcase - Test internal functions PASS: Test internal functions Ended 09-internal.scm === greg-tests Summary === # of testcases attempted 122 # of expected passes 122 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 Loading greg-tests/end.grg ... Loaded greg-tests/end.grg === Summary of all tests === # of tools 1 # of testcases attempted 122 # of expected passes 122 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 ObjectCache: Leaked 0003 refs to ObjectCache: Leaked 0003 refs to test_coot: coot test passed