testing with python unittest testing with python unittest currently we are here: /home/paule/autobuild/building/ubuntu-server_2018-01-02__T23_29_02/coot-0.8.9-pre /home/paule/autobuild/Linux-ubuntu-server-pre-release-gtk2-python/bin/coot --no-graphics --script python-tests/coot_unittest.py INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ INFO:: Reading coordinate file: /home/paule/autobuild/Linux-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 python-tests/coot_unittest.py Running python script python-tests/coot_unittest.py =============================================================== ==================== Testing ================================== =============================================================== WARNING:: unittest skip not avaliable!!!!!! ==== It seems CCP4_MASTER is setup === ==== CCP4_MASTER: /home/paule/ccp4 test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... INFO:: Command: (post-go-to-atom-window) ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... INFO:: Command: (close-molecule -2) ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... Molecule number -5 is not a valid model molecule ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2WF6.pdb" 1) WARNING:: Error reading /home/paule/data/greg-data/2WF6.pdb closing molecule number -1 INFO:: Command: (close-molecule -1) ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Command: (info-dialog "Oops, failed to create fragment. No atoms selected Incorrect atom specifier? "//A/100"") INFO:: pre_n_molecules 1 post_n_molecules 1 ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/ins-code-fragment-pre.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/paule/data/greg-data/ins-code-fragment-pre.pdb has been read. 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 1 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (set-go-to-atom-molecule 1) INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jan__2_23:44:44_2018_modification_0.pdb.gz INFO:: Command: (change-residue-number 1 "A" 68 "" 68 "A") INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jan__2_23:44:44_2018_modification_1.pdb.gz INFO:: Command: (change-residue-number 1 "A" 69 "" 68 "B") INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Tue_Jan__2_23:44:44_2018_modification_2.pdb.gz INFO:: Command: (change-residue-number 1 "A" 67 "" 68 "") pre and post ins codes: A INFO:: Command: (write-pdb-file 1 "post-ins-change.pdb") pass: ['A', 68, '', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'A', ' CA '] pass: ['A', 68, '', ' CA '] pass: ['A', 66, '', ' CA '] ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... WARNING:: Error reading bogus.map Read map bogus.map failed ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... WARNING:: Can't find file bogus.mtz INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.029 seconds to read MTZ file INFO:: 0.019 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.006 seconds for statistics Map mean: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.024 seconds for contour map INFO:: 0.101 seconds in total ok test07_1 (__main__.PdbMtzTestFunctions) Auto-read bad MTZ test ... WARNING:: file xx-missing.mtz does not exist got status: () >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 2:No such file or directory (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz got status: () ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... INFO:: map sigmas 0.311501026154 False ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 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:: 0.006 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:: 0.072 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: Command: (another-level-from-map-molecule-number 2) ok test09_1 (__main__.PdbMtzTestFunctions) db-main makes mainchain ... INFO:: Command: (handle-read-draw-molecule-with-recentre "." 1) WARNING:: Error reading . . is a directory. INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 4 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:: Command: (db-mainchain 4 "A" 10 20 "forward") ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... INFO:: Command: (set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.50) ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 6 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_23:44:45_2018_modification_0.pdb.gz INFO:: Command: (add-terminal-residue 6 "A" 1 1) INFO:: Command: (write-pdb-file 6 "regression-test-terminal-residue.pdb") INFO:: Command: (handle-read-draw-molecule-with-recentre "regression-test-terminal-residue.pdb" 1) INFO:: Reading coordinate file: regression-test-terminal-residue.pdb PDB file regression-test-terminal-residue.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 83/91 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 7 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/atom_selection_from_regression-test-terminal-residue.pdb_Tue_Jan__2_23:44:45_2018_modification_0.pdb.gz INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/frag-2wot.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 9 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... INFO:: Command: (n-chains 10) INFO:: Command: (chain_id 10 0) Sphere mol: there are 4 residues in chain B INFO:: Command: (resname-from-serial-number 10 "B" 0) INFO:: Command: (seqnum-from-serial-number 10 "B" 0) INFO:: Command: (insertion-code-from-serial-number 10 "B" 0) INFO:: Command: (resname-from-serial-number 10 "B" 1) INFO:: Command: (seqnum-from-serial-number 10 "B" 1) INFO:: Command: (insertion-code-from-serial-number 10 "B" 1) INFO:: Command: (resname-from-serial-number 10 "B" 2) INFO:: Command: (seqnum-from-serial-number 10 "B" 2) INFO:: Command: (insertion-code-from-serial-number 10 "B" 2) INFO:: Command: (resname-from-serial-number 10 "B" 3) INFO:: Command: (seqnum-from-serial-number 10 "B" 3) INFO:: Command: (insertion-code-from-serial-number 10 "B" 3) Found 20 sphere atoms ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... INFO:: Command: (go-to-view-number 0 1) ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 11 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_23:44:45_2018_modification_0.pdb.gz INFO:: Command: (delete-residue 11 "A" 42 "") residue info (should be False): False ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (set-rotation-centre 31.46 21.41 14.82) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:44:45_2018_modification_0.pdb.gz INFO:: Command: (delete-residue 12 "B" 10 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:44:45_2018_modification_1.pdb.gz INFO:: Command: (delete-residue 12 "B" 11 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:44:45_2018_modification_2.pdb.gz INFO:: Command: (delete-residue 12 "B" 12 "") ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/rotamer-test-fragment.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/rotamer-test-fragment.pdb PDB file /home/paule/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 13 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] ok test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/res098.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/res098.pdb PDB file /home/paule/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 14 read successfully DEBUG:: there were 0 types with no dictionary For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 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: 26.6475 Initial RMS Z values bonds: 0.22918 angles: 0.43392 torsions: N/A planes: 0.322152 non-bonded: 0 chiral vol: 0.162676 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 149) at 9.94502 Final Estimated RMS Z Scores: bonds: 0.0959081 angles: 0.665229 torsions: N/A planes: 0.648634 non-bonded: 0 chiral vol: 0.59145 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 2.093 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Tue_Jan__2_23:44:46_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 15 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 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: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.022 seconds for contour map INFO:: 0.072 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_23:44:46_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- 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_23:44:46_2018_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.9313 INFO:: Command: (auto-fit-best-rotamer 93 "A" "" "A" 15 16 1 0.01) ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb3knw.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3knw.ent PDB file /home/paule/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 185/199 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 17 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_23:44:46_2018_modification_0.pdb.gz se_1: [['SE ', ''], [0.7, 2.0, 'SE', ''], [58.8, 66.533, 0.047], 652] se_2: [['SE ', ''], [0.7, 2.0, 'SE', ''], [60.13112002923666, 69.34847968524429, -0.673518803101735], 652] ok test16_3 (__main__.PdbMtzTestFunctions) Hs are correctly swapped on a TYR ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1py3.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 18 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_23:44:46_2018_modification_0.pdb.gz INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP INFO:: 25 residues had their atoms swapped BL DEBUG:: results: [True, True, True, True] ok test16_4 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 19 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 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:: 0.022 seconds for contour map INFO:: 0.073 seconds in total INFO:: Command: (zero-occupancy-residue-range 19 "A" 37 37) DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:46_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 INFO:: Command: (close-molecule 19) INFO:: Command: (close-molecule 20) ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/paule/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 21 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_23:44:46_2018_modification_0.pdb.gz flipped 65 A ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (go-to-view-number 1 1) in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x2912d70 omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:44:47_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_23:44:47_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_23:44:47_2018_modification_2.pdb.gz INFO:: Command: (mutate 22 "A" 11 "" "GLY") 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: 5127.86 Initial RMS Z values bonds: 15.4585 angles: 7.12423 torsions: N/A planes: 2.18109 non-bonded: 126.244 chiral vol: 3.04463 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 55) at -3316.61 Final Estimated RMS Z Scores: bonds: 0.579221 angles: 0.761729 torsions: N/A planes: 2.37224 non-bonded: 0.050127 chiral vol: 0.418546 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.028 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_23:44:47_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_23:44:47_2018_modification_4.pdb.gz INFO:: Command: (mutate 22 "A" 11 "" "LEU") ------------ 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-cis-pep-12A_refmac0.pdb_Tue_Jan__2_23:44:47_2018_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.64758 INFO:: Command: (auto-fit-best-rotamer 11 "" "" "A" 22 2 1 1.00) ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring 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: -3565.14 Initial RMS Z values bonds: 0.912443 angles: 1.70476 torsions: N/A planes: 3.18344 non-bonded: 0.16175 chiral vol: 0.489919 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 39) at -3690.25 Final Estimated RMS Z Scores: bonds: 0.525868 angles: 0.686297 torsions: N/A planes: 2.44639 non-bonded: 0.0230965 chiral vol: 0.268097 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.12 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_23:44:47_2018_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Command: (write-pdb-file 22 "tmp-fixed-cis.pdb") ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 23 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 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: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.021 seconds for contour map INFO:: 0.071 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: -1605.78 Initial RMS Z values bonds: 1.67379 angles: 1.06965 torsions: N/A planes: 0.611295 non-bonded: 9.24559 chiral vol: 1.46202 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 60) at -1724.61 Final Estimated RMS Z Scores: bonds: 1.08485 angles: 1.21135 torsions: N/A planes: 0.5676 non-bonded: 0.0471055 chiral vol: 1.66418 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.302 Refinement elapsed time: 0.009 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:47_2018_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. refined moved: d= 0.702068414469 ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 25 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_23:44:47_2018_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 INFO:: Command: (set-go-to-atom-molecule 25) imol: 25 residues: [['A', 93, ''], ['A', 92, ''], ['A', 3, ''], ['A', 5, '']] INFO:: created 81 restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints 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: -8724.35 Initial RMS Z values bonds: 1.74258 angles: 1.26763 torsions: N/A planes: 0.838264 non-bonded: 0.000533565 chiral vol: 0.894378 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 4) at -9017.08 Final Estimated RMS Z Scores: bonds: 0.581819 angles: 0.623864 torsions: N/A planes: 0.62815 non-bonded: 2.4809e-05 chiral vol: 0.242586 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.596 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jan__2_23:44:47_2018_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. imol: 25 residues: [['A', 41, ''], ['A', 42, ''], ['A', 40, ''], ['A', 39, ''], ['A', 43, '']] INFO:: created 84 restraints created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints 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: -661.037 Initial RMS Z values bonds: 0.980695 angles: 1.01754 torsions: N/A planes: 1.78749 non-bonded: 4.74047 chiral vol: 10.2816 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -8497.64 Final Estimated RMS Z Scores: bonds: 1.19513 angles: 1.35912 torsions: N/A planes: 1.85058 non-bonded: 0.0128059 chiral vol: 1.09002 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.878 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Jan__2_23:44:47_2018_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. ======= got bond length 1.28288467658 ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 26 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 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: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 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: -1571.14 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 1.98457 non-bonded: 11.389 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 53) at -7364.12 Final Estimated RMS Z Scores: bonds: 1.11163 angles: 1.07648 torsions: N/A planes: 0.877498 non-bonded: 0.0214103 chiral vol: 0.785365 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.161 Refinement elapsed time: 0.091 refinement results: ['', 0, [['Bonds', 'Bonds: 1.112', 1.1116288900375366], ['Angles', 'Angles: 1.076', 1.076479434967041], ['Planes', 'Planes: 0.877', 0.8774980306625366], ['Non-bonded', 'Non-bonded: 0.146', 0.14632245898246765], ['Chirals', 'Chirals: 0.785', 0.7853654026985168]]] :::: ow factor 0.962742939591 ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/alt-conf-waters.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-waters.pdb PDB file /home/paule/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 28 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_23:44:48_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 ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... INFO:: Command: (update-go-to-atom-window-on-other-molecule-chosen) INFO:: Command: (set-go-to-atom-molecule 0) INFO:: Command: (set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B") ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/backrub-fragment.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/backrub-fragment.pdb PDB file /home/paule/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 29 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: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.362622 rms devi: 0.45613 max devi: 2.13962 min devi: 0.078632 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:: Command: (copy-molecule 29) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Tue_Jan__2_23:44:48_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Tue_Jan__2_23:44:48_2018_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "/RNASE3GMP/COMPLEX/FWT" "/RNASE3GMP/COMPLEX/PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.023 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.023 seconds for FFT INFO:: 0.005 seconds for statistics Map mean: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.021 seconds for contour map INFO:: 0.073 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/test-TER-OXT.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/test-TER-OXT.pdb PDB file /home/paule/data/greg-data/test-TER-OXT.pdb has been read. 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 32 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_23:44:48_2018_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45 INFO:: Command: (add-OXT-to-residue 32 14 "" "A") debug:: add_OXT_to_residue() returns istat 1 WARNING:: This residue already has an OXT - aborting INFO:: Command: (add-OXT-to-residue 32 14 "" "A") debug:: add_OXT_to_residue() returns istat 0 INFO:: Command: (write-pdb-file 32 "test-TER-OXT-added.pdb") found TER TER 25 ASP A 14 ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/val.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/val.pdb PDB file /home/paule/data/greg-data/val.pdb has been read. 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 33 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_23:44:48_2018_modification_0.pdb.gz INFO:: Command: (mutate 33 "C" 3 "" "HIS") INFO:: Command: (write-pdb-file 33 "his.pdb") ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2yie-frag.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2yie-frag.pdb PDB file /home/paule/data/greg-data/2yie-frag.pdb has been read. 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_2yie-frag.pdb_Tue_Jan__2_23:44:49_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0404315 rms devi: 0.0471732 max devi: 0.0832785 min devi: 0.0130055 INFO:: Command: (mutate-base 34 "X" 54 "" "C") INFO:: Command: (write-pdb-file 34 "2yie-mutated.pdb") ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/4f8g.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 35 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_23:44:49_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0434566 rms devi: 0.0477873 max devi: 0.073989 min devi: 0.0147744 INFO:: Command: (mutate-base 35 "A" 19 "" "DC") INFO:: Command: (write-pdb-file 35 "test-1.pdb") ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/4f8g.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices Molecule 36 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_23:44:49_2018_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0394451 rms devi: 0.0444615 max devi: 0.0694865 min devi: 0.0151341 INFO:: Command: (mutate-base 36 "A" 10 "" "DT") INFO:: Command: (write-pdb-file 36 "test-2.pdb") ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... failed to delete residue atoms A 88 :A: INFO:: Command: (delete-residue-with-full_spec 0 1 "A" 88 "" "A") ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 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:: 0.005 seconds for statistics Map mean: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.018 seconds for contour map INFO:: 0.069 seconds in total INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.023 seconds to read MTZ file INFO:: 0.032 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.18457e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.027 seconds for contour map INFO:: 0.124 seconds in total INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 39 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.00140371 st.d: 0.305546 Map statistics: min: -0.895738, max: 2.76376 -0.849994 7 -0.758507 47 -0.66702 345 -0.575532 1966 -0.484045 7547 -0.392558 21145 -0.30107 36984 -0.209583 49747 -0.118096 62502 -0.0266081 78146 0.0648792 56227 0.156367 31741 0.247854 15372 0.339341 9396 0.430829 7278 0.522316 6354 0.613803 5287 0.705291 4622 0.796778 3865 0.888265 3168 0.979753 2366 1.07124 1769 1.16273 1258 1.25421 879 1.3457 637 1.43719 417 1.52868 237 1.62016 135 1.71165 69 1.80314 46 1.89463 18 1.98611 8 2.0776 2 2.16909 6 2.26058 2 2.35206 0 2.44355 1 2.53504 3 2.62653 0 2.71801 1 2.8095 0 INFO:: Command: (atom_info_string 39 A 20 CA ) INFO:: Command: (atom_info_string 39 A 21 CA ) INFO:: Command: (atom_info_string 39 A 22 CA ) INFO:: Command: (atom_info_string 39 A 23 CA ) INFO:: Command: (atom_info_string 39 A 24 CA ) INFO:: Command: (atom_info_string 39 A 25 CA ) INFO:: Command: (atom_info_string 39 A 26 CA ) INFO:: Command: (atom_info_string 39 A 27 CA ) INFO:: Command: (atom_info_string 39 A 28 CA ) INFO:: Command: (atom_info_string 39 A 29 CA ) INFO:: Command: (atom_info_string 39 A 30 CA ) INFO:: Command: (atom_info_string 39 A 1 CA ) INFO:: Command: (atom_info_string 39 A 2 CA ) INFO:: Command: (atom_info_string 39 A 3 CA ) INFO:: Command: (atom_info_string 39 A 4 CA ) INFO:: Command: (atom_info_string 39 A 5 CA ) INFO:: Command: (atom_info_string 39 A 6 CA ) INFO:: Command: (atom_info_string 39 A 7 CA ) INFO:: Command: (atom_info_string 39 A 8 CA ) INFO:: Command: (atom_info_string 39 A 9 CA ) INFO:: Command: (atom_info_string 39 A 10 CA ) high-values: [0.7880393862724304, 0.9311162829399109, 0.9948475360870361, 1.0713924169540405, 0.7348382472991943, 0.8019416332244873, 0.6376815438270569, 0.6461937427520752, 0.952126145362854, 0.9289178252220154, 0.9664078950881958] low values: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] Map statistics: mean: -0.001364 st.d: 0.0602937 Map statistics: min: -2.97717, max: 0.74609 -2.93063 1 -2.83755 1 -2.74447 1 -2.65139 2 -2.55831 2 -2.46522 0 -2.37214 2 -2.27906 1 -2.18598 1 -2.0929 4 -1.99982 2 -1.90673 3 -1.81365 4 -1.72057 4 -1.62749 8 -1.53441 11 -1.44133 15 -1.34825 33 -1.25516 33 -1.16208 49 -1.069 65 -0.975919 120 -0.882838 145 -0.789756 159 -0.696674 202 -0.603593 249 -0.510511 275 -0.41743 291 -0.324348 411 -0.231267 440 -0.138185 581 -0.0451035 300752 0.0479781 101991 0.14106 1213 0.234141 1098 0.327223 767 0.420304 463 0.513386 156 0.606468 36 0.699549 8 0.792631 1 diff-high-values: [0.0032140458934009075, 0.005670706741511822, 0.0031834905967116356, 0.0036503991577774286, 0.005187051370739937, 0.0033501957077533007, 0.0024679440539330244, 0.007025451865047216, 0.004253388848155737, -0.0006197448819875717, 0.0035091182217001915] diff-low-values: [-0.5327256321907043, -0.9398592710494995, -0.7048763632774353, -0.827702522277832, -0.8482539653778076, -1.0417752265930176, -1.1633360385894775, -1.1859604120254517, -0.8826918005943298, -0.8691443204879761] ok test29_1 (__main__.PdbMtzTestFunctions) Skeletonize a map ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 42 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 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: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.022 seconds for contour map INFO:: 0.072 seconds in total INFO:: Command: (close-molecule 42) INFO:: Command: (close-molecule 43) ok test29_2 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.024 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.022 seconds for FFT INFO:: 0.005 seconds for statistics Map mean: ........ 9.02233e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.021 seconds for contour map INFO:: 0.073 seconds in total INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.023 seconds to read MTZ file INFO:: 0.044 seconds to initialize map INFO:: 0.047 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.14601e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.048 seconds for contour map INFO:: 0.172 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: 1.6876e-07 st.d: 0.311081 Map statistics: min: -0.894093, max: 3.00714 -0.845327 8 -0.747797 64 -0.650266 542 -0.552735 3067 -0.455204 12045 -0.357673 29986 -0.260143 46658 -0.162612 61563 -0.0650809 73639 0.0324499 68489 0.129981 41912 0.227511 19494 0.325042 11050 0.422573 8221 0.520104 7074 0.617635 5839 0.715166 5071 0.812696 4183 0.910227 3295 1.00776 2384 1.10529 1722 1.20282 1175 1.30035 843 1.39788 560 1.49541 325 1.59294 179 1.69047 90 1.788 59 1.88554 23 1.98307 9 2.0806 8 2.17813 6 2.27566 2 2.37319 2 2.47072 4 2.56825 3 2.66578 2 2.76331 2 2.86084 1 2.95837 0 3.0559 1 Map statistics: mean: -1.67858e-07 st.d: 0.00107625 Map statistics: min: -0.0109431, max: 0.0109034 -0.01067 1 -0.0101239 1 -0.00957771 0 -0.00903155 1 -0.00848539 3 -0.00793922 2 -0.00739306 4 -0.0068469 7 -0.00630074 25 -0.00575458 37 -0.00520842 103 -0.00466225 260 -0.00411609 640 -0.00356993 1269 -0.00302377 2611 -0.00247761 5434 -0.00193144 10529 -0.00138528 21799 -0.000839121 51978 -0.000292959 109495 0.000253203 110465 0.000799365 52013 0.00134553 20447 0.00189169 9606 0.00243785 5236 0.00298401 2974 0.00353017 1857 0.00407634 1167 0.0046225 683 0.00516866 388 0.00571482 223 0.00626098 139 0.00680714 86 0.00735331 56 0.00789947 25 0.00844563 16 0.00899179 7 0.00953795 4 0.0100841 4 0.0106303 4 0.0111764 1 INFO:: map sigmas: normal 0.311081498861 and diff-map: 0.00107625476085 ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/multi-carbo-coot-3.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/multi-carbo-coot-3.pdb PDB file /home/paule/data/greg-data/multi-carbo-coot-3.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 48 read successfully DEBUG:: there were 2 types with no dictionary bond-length: 2.2472994905 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: 2651.72 Initial RMS Z values bonds: 6.1616 angles: 2.85281 torsions: N/A planes: 0.0835273 non-bonded: 0.225366 chiral vol: 0.903463 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 887) at 15.9904 Final Estimated RMS Z Scores: bonds: 0.100855 angles: 0.422509 torsions: N/A planes: 0.0264038 non-bonded: 0.000189765 chiral vol: 0.156126 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.889 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-3.pdb_Tue_Jan__2_23:44:51_2018_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. bond-length: 1.44437913592 ok test30_1 (__main__.PdbMtzTestFunctions) Refine an NAG-ASN Link ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb PDB file /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 3 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 4/110 Molecule 49 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.023 seconds to read MTZ file INFO:: 0.011 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.04051e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 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_23:44:51_2018_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:44:51_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_23:44:51_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 930 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: 67178.9 Initial RMS Z values bonds: 0.360748 angles: 0.606408 torsions: N/A planes: 0.68341 non-bonded: 72.4293 chiral vol: 0.444926 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 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 47) at -68.0567 Final Estimated RMS Z Scores: bonds: 2.45396 angles: 1.79602 torsions: N/A planes: 2.25616 non-bonded: 0.0523821 chiral vol: 0.990121 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): 8.069 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:44:51_2018_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. 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_23:44:51_2018_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 685 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: 2876.76 Initial RMS Z values bonds: 2.45396 angles: 1.79602 torsions: N/A planes: 2.25616 non-bonded: 4.4334 chiral vol: 0.990121 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 Minimum found (iteration number 78) at -68.0477 Final Estimated RMS Z Scores: bonds: 2.45286 angles: 1.80176 torsions: N/A planes: 2.2544 non-bonded: 0.0711464 chiral vol: 0.990123 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): 8.649 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:44:51_2018_modification_5.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 678 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: -68.0477 Initial RMS Z values bonds: 2.45286 angles: 1.80176 torsions: N/A planes: 2.2544 non-bonded: 0.0718809 chiral vol: 0.990123 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -68.0499 Final Estimated RMS Z Scores: bonds: 2.4524 angles: 1.80163 torsions: N/A planes: 2.25378 non-bonded: 0.0719848 chiral vol: 0.990544 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): 8.697 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Jan__2_23:44:51_2018_modification_6.pdb.gz INFO:: replace_coords: 22 atoms updated. ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-VAL.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-VAL.pdb PDB file /home/paule/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 51 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: 4.99701 Initial RMS Z values bonds: 0.542493 angles: 0.164062 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.451586 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.248183 Final Estimated RMS Z Scores: bonds: 0.0122184 angles: 0.0948581 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.145399 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.041 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:44:53_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 51 INFO:: Command: (set-undo-molecule 51) INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:44:53_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_23:44:53_2018_modification_0.pdb.gz PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:44:53_2018_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 INFO:: Command: (apply-undo) 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: 4.99701 Initial RMS Z values bonds: 0.542493 angles: 0.164062 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.451586 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.248183 Final Estimated RMS Z Scores: bonds: 0.0122184 angles: 0.0948581 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.145399 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.07 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Tue_Jan__2_23:44:53_2018_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. ok test32_0 (__main__.PdbMtzTestFunctions) Test for mangling of hydrogen names from a PDB v 3.0 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. 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 52 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: 903.063 Initial RMS Z values bonds: 5.62114 angles: 3.43297 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.753357 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 165) at 0.474695 Final Estimated RMS Z Scores: bonds: 0.00942912 angles: 0.121017 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.138512 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.468 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_23:44:53_2018_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... looping over restraint plane restraint: [plane-restraint: plan {12 atoms} : CB 0.02: : CG 0.02: : CD1 0.02: : CE1 0.02: : CZ 0.02: : CE2 0.02: : CD2 0.02: : OH 0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ] INFO:: Command: (update-go-to-atom-window-on-new-mol) 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: 1505.91 Initial RMS Z values bonds: 1.1515 angles: 0.847578 torsions: N/A planes: 3.05577 non-bonded: 81.9061 chiral vol: 0.757848 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 38) at -1706.19 Final Estimated RMS Z Scores: bonds: 0.786872 angles: 0.635771 torsions: N/A planes: 0.501007 non-bonded: 0.0206674 chiral vol: 0.539584 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.513 Refinement elapsed time: 0.016 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:44:53_2018_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. Bond-length: 2.62204416269 pass intermediate 2.8 tolerance test looping over restraint plane restraint: [plane-restraint: plan {12 atoms} : CB 0.02: : CG 0.02: : CD1 0.02: : CE1 0.02: : CZ 0.02: : CE2 0.02: : CD2 0.02: : OH 0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ] 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: 838.864 Initial RMS Z values bonds: 14.585 angles: 0.635771 torsions: N/A planes: 0.501007 non-bonded: 0 chiral vol: 0.539584 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -1751.03 Final Estimated RMS Z Scores: bonds: 0.66937 angles: 0.644341 torsions: N/A planes: 1.14532 non-bonded: 0 chiral vol: 0.584933 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.531 Refinement elapsed time: 0.01 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:44:53_2018_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. OK plane atom CB Bond-length: 1.51838520717 ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... INFO:: wrote mmCIF "coot-test-ala.cif" ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-ACT.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 54 read successfully DEBUG:: there were 1 types with no dictionary Welcome to Coot looping over restraint plane restraint: [plane-restraint: plan-1 {4 atoms} : C 0.02: : O 0.02: : OXT 0.02: : CH3 0.02: ] 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: 0.0119892 angles: 0.00653967 torsions: N/A planes: 0 non-bonded: 689.927 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 10) at -385.659 Final Estimated RMS Z Scores: bonds: 0.157553 angles: 0.0363384 torsions: N/A planes: 0.0853755 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 10.054 Refinement elapsed time: 0.013 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Tue_Jan__2_23:44:54_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 55 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_23:44:54_2018_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:54_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_23:44:54_2018_modification_2.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:54_2018_modification_3.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:54_2018_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:54_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_23:44:54_2018_modification_6.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:54_2018_modification_7.pdb.gz INFO:: Command: (n-chains 55) INFO:: Command: (chain_id 55 0) INFO:: Command: (chain_id 55 1) INFO:: Command: (chain_id 55 2) INFO:: Command: (chain_id 55 3) INFO:: Command: (chain_id 55 4) INFO:: Command: (chain_id 55 5) INFO:: Command: (chain_id 55 6) INFO:: Command: (chain_id 55 7) INFO:: Command: (chain_id 55 8) ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: Command: (copy-molecule 0) INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Jan__2_23:44:54_2018_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:54_2018_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Command: (replace-fragement 56 57 "//A70-80") distances: [20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966] ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... found 6 neighbours [['A', 39, ''], ['A', 41, ''], ['A', 38, ''], ['B', 61, ''], ['A', 42, ''], ['B', 60, '']] found 0 neighbours [] ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 58 read successfully DEBUG:: there were 0 types with no dictionary ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:55_2018_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 59 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (turn-off-backup 59) INFO:: Command: (rotamer-score 59 "A" 28 "") Rotamer 0 : m-85 100.0 INFO:: Command: (rotamer-score 59 "A" 28 "") Rotamer 1 : t80 90.1668395996 INFO:: Command: (rotamer-score 59 "A" 28 "") Rotamer 2 : p90 50.7077865601 INFO:: Command: (rotamer-score 59 "A" 28 "") Rotamer 3 : m -30 21.4231548309 INFO:: Command: (rotamer-score 59 "A" 28 "") Rotamer 4 : m -30 21.4231548309 INFO:: Command: (turn-on-backup 59) ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 50/87 Molecule 60 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 60 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -0.5 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 ||||||| |||||||||| |||||||| |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 163.5 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_23:44:55_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: 244810760 "A" 1 ""] -> ASP [spec: 244810760 "A" 2 ""] -> VAL [spec: 244810760 "A" 3 ""] -> SER [spec: 244810760 "A" 11 ""] -> LEU [spec: 244810760 "A" 12 ""] -> PRO [spec: 244810760 "A" 13 ""] -> PRO [spec: 244810760 "A" 62 ""] -> PRO [spec: 244810760 "A" 63 ""] -> GLY Deletions: [spec: 244810760 "A" 24 ""] [spec: 244810760 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions INFO:: Command: (write-pdb-file 60 "mutated.pdb") ::::: [60, 'A', 1, ''] False False ::::: [60, 'A', 4, ''] True True ::::: [60, 'A', 59, ''] True True ::::: [60, 'A', 60, ''] False False ::::: [60, 'A', 61, ''] False False ::::: [60, 'A', 93, ''] True True ::::: [60, 'A', 94, ''] False False ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 61 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_23:44:56_2018_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 61 "A" 10 20 100) INFO:: Command: (seqnum-from-serial-number 61 "A" 90) INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 62 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_23:44:56_2018_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 62 "A" 10 20 -100) INFO:: Command: (seqnum-from-serial-number 62 "A" 0) ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb3hfl.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3hfl.ent PDB file /home/paule/data/greg-data/pdb3hfl.ent has been read. 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 63 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.02 seconds to read MTZ file INFO:: 0.006 seconds to initialize map INFO:: 0.013 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 7.46232e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.008 seconds for contour map INFO:: 0.049 seconds in total INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Tue_Jan__2_23:44:57_2018_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.83405 INFO:: Command: (auto-fit-best-rotamer 52 "" "A" "H" 63 64 0 0.00) INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Tue_Jan__2_23:44:57_2018_modification_1.pdb.gz ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 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_23:44:57_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Jan__2_23:44:57_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269035 rms devi: 0.337196 max devi: 0.547544 min devi: 0.0817551 INFO:: Command: (mutate-base 65 "A" 2 "" "C") mutated base to type C - was A INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 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_23:44:57_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Jan__2_23:44:57_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269035 rms devi: 0.337196 max devi: 0.547544 min devi: 0.0817551 INFO:: Command: (mutate-base 66 "A" 2 "" "Cr") mutated base to type Cr - was A ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0.00589883 rms devi: 0.00670957 max devi: 0.0101325 min devi: 0.00258111 INFO:: 5 matched atoms had: mean devi: 0.00725623 rms devi: 0.00778801 max devi: 0.0125644 min devi: 0.00456024 INFO:: 5 matched atoms had: mean devi: 0.271793 rms devi: 0.336384 max devi: 0.533839 min devi: 0.0878288 INFO:: 5 matched atoms had: mean devi: 0.26776 rms devi: 0.326512 max devi: 0.505569 min devi: 0.10459 INFO:: 5 matched atoms had: mean devi: 0.271823 rms devi: 0.336416 max devi: 0.53388 min devi: 0.0879009 INFO:: 5 matched atoms had: mean devi: 0.267791 rms devi: 0.326544 max devi: 0.505617 min devi: 0.104522 INFO:: 5 matched atoms had: mean devi: 0.00717866 rms devi: 0.00770023 max devi: 0.0124098 min devi: 0.00457508 INFO:: 5 matched atoms had: mean devi: 0.00574436 rms devi: 0.00657052 max devi: 0.0099594 min devi: 0.0024248 INFO:: 5 matched atoms had: mean devi: 0.271762 rms devi: 0.336353 max devi: 0.533797 min devi: 0.0877567 INFO:: 5 matched atoms had: mean devi: 0.267729 rms devi: 0.326479 max devi: 0.505521 min devi: 0.104657 INFO:: 5 matched atoms had: mean devi: 0.00585391 rms devi: 0.00666923 max devi: 0.0100827 min devi: 0.00253528 INFO:: 5 matched atoms had: mean devi: 0.00722485 rms devi: 0.00775255 max devi: 0.0125025 min devi: 0.00456535 INFO:: 5 matched atoms had: mean devi: 0.00580961 rms devi: 0.00662938 max devi: 0.0100332 min devi: 0.00249036 INFO:: 5 matched atoms had: mean devi: 0.00719394 rms devi: 0.00771755 max devi: 0.0124407 min devi: 0.00457156 INFO:: 5 matched atoms had: mean devi: 0.267807 rms devi: 0.326561 max devi: 0.505641 min devi: 0.104488 INFO:: 5 matched atoms had: mean devi: 0.27187 rms devi: 0.336463 max devi: 0.533942 min devi: 0.088009 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_23:44:57_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270191 rms devi: 0.336363 max devi: 0.538427 min devi: 0.0854029 INFO:: Command: (mutate-base 67 "A" 2 "" "DC") mutated base to type DC INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.271895 rms devi: 0.336278 max devi: 0.534478 min devi: 0.0923473 INFO:: Command: (mutate-base 67 "A" 2 "" "DG") mutated base to type DG INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043292 rms devi: 0.00481764 max devi: 0.00738267 min devi: 0.00186162 INFO:: Command: (mutate-base 67 "A" 2 "" "DA") mutated base to type DA INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.265718 rms devi: 0.326008 max devi: 0.501859 min devi: 0.0926641 INFO:: Command: (mutate-base 67 "A" 2 "" "DT") mutated base to type DT INFO:: 5 matched atoms had: mean devi: 0.00589883 rms devi: 0.00670957 max devi: 0.0101325 min devi: 0.00258111 INFO:: 5 matched atoms had: mean devi: 0.00725623 rms devi: 0.00778801 max devi: 0.0125644 min devi: 0.00456024 INFO:: 5 matched atoms had: mean devi: 0.271793 rms devi: 0.336384 max devi: 0.533839 min devi: 0.0878288 INFO:: 5 matched atoms had: mean devi: 0.26776 rms devi: 0.326512 max devi: 0.505569 min devi: 0.10459 INFO:: 5 matched atoms had: mean devi: 0.271823 rms devi: 0.336416 max devi: 0.53388 min devi: 0.0879009 INFO:: 5 matched atoms had: mean devi: 0.267791 rms devi: 0.326544 max devi: 0.505617 min devi: 0.104522 INFO:: 5 matched atoms had: mean devi: 0.00717866 rms devi: 0.00770023 max devi: 0.0124098 min devi: 0.00457508 INFO:: 5 matched atoms had: mean devi: 0.00574436 rms devi: 0.00657052 max devi: 0.0099594 min devi: 0.0024248 INFO:: 5 matched atoms had: mean devi: 0.271762 rms devi: 0.336353 max devi: 0.533797 min devi: 0.0877567 INFO:: 5 matched atoms had: mean devi: 0.267729 rms devi: 0.326479 max devi: 0.505521 min devi: 0.104657 INFO:: 5 matched atoms had: mean devi: 0.00585391 rms devi: 0.00666923 max devi: 0.0100827 min devi: 0.00253528 INFO:: 5 matched atoms had: mean devi: 0.00722485 rms devi: 0.00775255 max devi: 0.0125025 min devi: 0.00456535 INFO:: 5 matched atoms had: mean devi: 0.00580961 rms devi: 0.00662938 max devi: 0.0100332 min devi: 0.00249036 INFO:: 5 matched atoms had: mean devi: 0.00719394 rms devi: 0.00771755 max devi: 0.0124407 min devi: 0.00457156 INFO:: 5 matched atoms had: mean devi: 0.267807 rms devi: 0.326561 max devi: 0.505641 min devi: 0.104488 INFO:: 5 matched atoms had: mean devi: 0.27187 rms devi: 0.336463 max devi: 0.533942 min devi: 0.088009 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_23:44:57_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270191 rms devi: 0.336363 max devi: 0.538427 min devi: 0.0854029 INFO:: Command: (mutate-base 68 "A" 2 "" "Cd") mutated base to type Cd INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.271895 rms devi: 0.336278 max devi: 0.534478 min devi: 0.0923473 INFO:: Command: (mutate-base 68 "A" 2 "" "Gd") mutated base to type Gd INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043292 rms devi: 0.00481764 max devi: 0.00738267 min devi: 0.00186162 INFO:: Command: (mutate-base 68 "A" 2 "" "Ad") mutated base to type Ad INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Jan__2_23:44:57_2018_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.265718 rms devi: 0.326008 max devi: 0.501859 min devi: 0.0926641 INFO:: Command: (mutate-base 68 "A" 2 "" "Td") mutated base to type Td ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: Command: (copy-molecule 0) INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:57_2018_modification_0.pdb.gz INFO:: Command: (mutate 69 "A" 32 "" "LYS") ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/some-waters-with-ter.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/some-waters-with-ter.pdb PDB file /home/paule/data/greg-data/some-waters-with-ter.pdb has been read. 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 70 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (set-rotation-centre 3.00 4.00 5.00) INFO:: backup file coot-backup/_home_paule_data_greg-data_some-waters-with-ter.pdb_Tue_Jan__2_23:44:57_2018_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (write-pdb-file 70 "tmp-with-new-water.pdb") ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tm+some-waters.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tm+some-waters.pdb PDB file /home/paule/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 71 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 0.2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.311501 INFO:: Using density cut-off: 0.0623002 (0.2 sigma) (mean -0.0338336 stdev: 0.14627) 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 = ( 27.82, 31.44, 8.887) is too big to be water INFO:: cluster at xyz = ( 70.04, 19.1, 18.63) is too big to be water INFO:: cluster at xyz = ( 69.25, 5.345, 11.11) is too big to be water INFO:: cluster at xyz = ( 52.69, 10.79, 11.51) is too big to be water INFO:: cluster at xyz = ( 72.02, 12.27, 14.68) is too big to be water INFO:: cluster at xyz = ( 39.69, 8.165, 19.55) is too big to be water INFO:: cluster at xyz = ( 53.3, -4.968, -2.722) is too big to be water INFO:: cluster at xyz = ( 40.99, 7.049, 16.27) is too big to be water INFO:: cluster at xyz = ( 25.71, 4.246, 5.745) is too big to be water INFO:: found 46 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_tm+some-waters.pdb_Tue_Jan__2_23:44:58_2018_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Command: (write-pdb-file 71 "auto-waters.pdb") ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 72 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_23:44:58_2018_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:44:58_2018_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/water-test-no-cell.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/water-test-no-cell.pdb PDB file /home/paule/data/greg-data/water-test-no-cell.pdb has been read. 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 73 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_23:45:01_2018_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pathological-water-test.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pathological-water-test.pdb PDB file /home/paule/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 74 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_23:45:01_2018_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: Command: (write-pdb-file 74 "waters-moved-failure.pdb") ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: Command: (copy-molecule 0) INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.023 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: ........ 1.04051e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.013 seconds for contour map INFO:: 0.056 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_23:45:01_2018_modification_0.pdb.gz INFO:: Command: (add-terminal-residue 75 "A" 93 1) ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: Command: (copy-molecule 0) DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 77 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 77 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: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 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_23:45:01_2018_modification_0.pdb.gz ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 78 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (turn-off-backup 78) 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain) INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 43.60 8.69 12.91) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 45.60 8.69 12.91) 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 47.60 8.69 12.91) 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 49.60 8.69 12.91) 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 51.60 8.69 12.91) INFO:: Command: (renumber-residue-range 78 "D" 1 5 10) 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 53.60 8.69 12.91) 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 55.60 8.69 12.91) 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 57.60 8.69 12.91) 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 59.60 8.69 12.91) 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 61.60 8.69 12.91) INFO:: Command: (renumber-residue-range 78 "E" 11 15 5) 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 63.60 8.69 12.91) 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 65.60 8.69 12.91) 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 67.60 8.69 12.91) 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 69.60 8.69 12.91) 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 71.60 8.69 12.91) INFO:: Command: (renumber-residue-range 78 "F" 16 20 2) INFO:: Command: (n-chains 78) INFO:: Command: (chain_id 78 0) INFO:: Command: (chain_id 78 1) INFO:: Command: (chain_id 78 2) INFO:: Command: (chain_id 78 3) INFO:: Command: (chain_id 78 4) INFO:: Command: (is-solvent-chain-p 78 "A") INFO:: Command: (is-solvent-chain-p 78 "B") INFO:: Command: (is-solvent-chain-p 78 "D") INFO:: Command: (is-solvent-chain-p 78 "E") INFO:: Command: (is-solvent-chain-p 78 "F") INFO:: Command: (resname-from-serial-number 78 "D" 0) INFO:: Command: (seqnum-from-serial-number 78 "D" 0) INFO:: Command: (insertion-code-from-serial-number 78 "D" 0) INFO:: Command: (resname-from-serial-number 78 "D" 1) INFO:: Command: (seqnum-from-serial-number 78 "D" 1) INFO:: Command: (insertion-code-from-serial-number 78 "D" 1) INFO:: Command: (resname-from-serial-number 78 "D" 2) INFO:: Command: (seqnum-from-serial-number 78 "D" 2) INFO:: Command: (insertion-code-from-serial-number 78 "D" 2) INFO:: Command: (resname-from-serial-number 78 "D" 3) INFO:: Command: (seqnum-from-serial-number 78 "D" 3) INFO:: Command: (insertion-code-from-serial-number 78 "D" 3) INFO:: Command: (resname-from-serial-number 78 "D" 4) INFO:: Command: (seqnum-from-serial-number 78 "D" 4) INFO:: Command: (insertion-code-from-serial-number 78 "D" 4) INFO:: Command: (does-residue-exist-p 78 D 1 ) INFO:: Command: (does-residue-exist-p 78 D 2 ) INFO:: Command: (does-residue-exist-p 78 D 3 ) INFO:: Command: (does-residue-exist-p 78 D 4 ) INFO:: Command: (does-residue-exist-p 78 D 5 ) INFO:: Command: (resname-from-serial-number 78 "E" 0) INFO:: Command: (seqnum-from-serial-number 78 "E" 0) INFO:: Command: (insertion-code-from-serial-number 78 "E" 0) INFO:: Command: (resname-from-serial-number 78 "E" 1) INFO:: Command: (seqnum-from-serial-number 78 "E" 1) INFO:: Command: (insertion-code-from-serial-number 78 "E" 1) INFO:: Command: (resname-from-serial-number 78 "E" 2) INFO:: Command: (seqnum-from-serial-number 78 "E" 2) INFO:: Command: (insertion-code-from-serial-number 78 "E" 2) INFO:: Command: (resname-from-serial-number 78 "E" 3) INFO:: Command: (seqnum-from-serial-number 78 "E" 3) INFO:: Command: (insertion-code-from-serial-number 78 "E" 3) INFO:: Command: (resname-from-serial-number 78 "E" 4) INFO:: Command: (seqnum-from-serial-number 78 "E" 4) INFO:: Command: (insertion-code-from-serial-number 78 "E" 4) INFO:: Command: (does-residue-exist-p 78 E 1 ) INFO:: Command: (does-residue-exist-p 78 E 2 ) INFO:: Command: (does-residue-exist-p 78 E 3 ) INFO:: Command: (does-residue-exist-p 78 E 4 ) INFO:: Command: (does-residue-exist-p 78 E 5 ) INFO:: Command: (resname-from-serial-number 78 "F" 0) INFO:: Command: (seqnum-from-serial-number 78 "F" 0) INFO:: Command: (insertion-code-from-serial-number 78 "F" 0) INFO:: Command: (resname-from-serial-number 78 "F" 1) INFO:: Command: (seqnum-from-serial-number 78 "F" 1) INFO:: Command: (insertion-code-from-serial-number 78 "F" 1) INFO:: Command: (resname-from-serial-number 78 "F" 2) INFO:: Command: (seqnum-from-serial-number 78 "F" 2) INFO:: Command: (insertion-code-from-serial-number 78 "F" 2) INFO:: Command: (resname-from-serial-number 78 "F" 3) INFO:: Command: (seqnum-from-serial-number 78 "F" 3) INFO:: Command: (insertion-code-from-serial-number 78 "F" 3) INFO:: Command: (resname-from-serial-number 78 "F" 4) INFO:: Command: (seqnum-from-serial-number 78 "F" 4) INFO:: Command: (insertion-code-from-serial-number 78 "F" 4) INFO:: Command: (does-residue-exist-p 78 F 1 ) INFO:: Command: (does-residue-exist-p 78 F 2 ) INFO:: Command: (does-residue-exist-p 78 F 3 ) INFO:: Command: (does-residue-exist-p 78 F 4 ) INFO:: Command: (does-residue-exist-p 78 F 5 ) INFO:: Command: (renumber-residue-range 78 "E" 1 5 5) INFO:: Command: (renumber-residue-range 78 "F" 1 5 10) INFO:: Command: (turn-on-backup 78) INFO:: Command: (n-chains 78) INFO:: Command: (chain_id 78 2) INFO:: Command: (seqnum-from-serial-number 78 "D" 0) INFO:: Command: (seqnum-from-serial-number 78 "D" 14) ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 79 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-ACT.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 80 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-NPO.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 81 read successfully DEBUG:: there were 1 types with no dictionary -------- starting chain list ----------- INFO:: Command: (n-chains 79) INFO:: Command: (chain_id 79 0) INFO:: Command: (chain_id 79 1) INFO:: Command: (chain_id 79 2) INFO:: Command: (chain_id 79 3) INFO:: Command: (chain_id 79 4) ['A', 'B', 'C', 'D', ''] -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0 0 0.333333 pre-trans: 0 0 0 INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.5724,-20.4973,95.468) B-factor: 45.26 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (64.4244,-37.8536,121.388) B-factor: 88.52 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.49888 rms devi: 2.79624 max devi: 6.68599 min devi: 0.440067 find_ncs_matrix returns (LSQ) | 0.8045, 0.069, 0.59| | 0.5435, 0.315, -0.778| | -0.2395, 0.9466, 0.2159| ( -57.32, 43.57, 131.4) INFO:: NCS chain comparison 66/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.5724,-20.4973,95.468) B-factor: 45.26 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (-18.2586,-63.0428,111.425) B-factor: 50.76 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.97132 rms devi: 2.1729 max devi: 4.54109 min devi: 0.429522 find_ncs_matrix returns (LSQ) | -0.5596, -0.8266, 0.06065| | -0.8239, 0.5468, -0.1492| | 0.09015, -0.1334, -0.9869| ( -4.436, 16.92, 204.3) INFO:: NCS chain comparison 61/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.5724,-20.4973,95.468) B-factor: 45.26 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (-0.291112,-72.4822,94.469) B-factor: 78.35 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.70416 rms devi: 4.0859 max devi: 9.43828 min devi: 0.285802 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:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (n-chains 79) INFO:: Command: (chain_id 79 0) INFO:: Command: (chain_id 79 1) INFO:: Command: (chain_id 79 2) INFO:: Command: (chain_id 79 3) INFO:: Command: (chain_id 79 4) INFO:: Command: (chain_id 79 5) INFO:: Command: (chain_id 79 6) INFO:: Command: (chain_id 79 7) INFO:: Command: (chain_id 79 8) INFO:: Command: (chain_id 79 9) INFO:: Command: (chain_id 79 10) INFO:: Command: (chain_id 79 11) ['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K'] INFO:: Command: (write-pdb-file 79 "sym-merged.pdb") ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: Command: (copy-molecule 0) INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: Command: (copy-molecule 0) INFO:: Matching/moving molecule number 84 to 83 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.0353197 rms devi: 0.0377881 max devi: 0.0545286 min devi: 0.016676 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_23:45:03_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 85 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1py3.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 86 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 85 to 86 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.502333 rms devi: 0.593803 max devi: 1.67852 min devi: 0.0431788 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_23:45:04_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 87 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_23:45:04_2018_modification_0.pdb.gz INFO:: Command: (set-residue-name 87 "A" 37 "" "FRE") INFO:: Command: (n-chains 87) INFO:: Command: (chain_id 87 0) INFO:: Command: (chain_id 87 1) INFO:: Command: (seqnum-from-serial-number 87 "A" 0) INFO:: Command: (insertion-code-from-serial-number 87 "A" 0) INFO:: Command: (seqnum-from-serial-number 87 "A" 1) INFO:: Command: (insertion-code-from-serial-number 87 "A" 1) INFO:: Command: (seqnum-from-serial-number 87 "A" 2) INFO:: Command: (insertion-code-from-serial-number 87 "A" 2) INFO:: Command: (seqnum-from-serial-number 87 "A" 3) INFO:: Command: (insertion-code-from-serial-number 87 "A" 3) INFO:: Command: (seqnum-from-serial-number 87 "A" 4) INFO:: Command: (insertion-code-from-serial-number 87 "A" 4) INFO:: Command: (seqnum-from-serial-number 87 "A" 5) INFO:: Command: (insertion-code-from-serial-number 87 "A" 5) INFO:: Command: (seqnum-from-serial-number 87 "A" 6) INFO:: Command: (insertion-code-from-serial-number 87 "A" 6) INFO:: Command: (seqnum-from-serial-number 87 "A" 7) INFO:: Command: (insertion-code-from-serial-number 87 "A" 7) INFO:: Command: (seqnum-from-serial-number 87 "A" 8) INFO:: Command: (insertion-code-from-serial-number 87 "A" 8) INFO:: Command: (seqnum-from-serial-number 87 "A" 9) INFO:: Command: (insertion-code-from-serial-number 87 "A" 9) INFO:: Command: (seqnum-from-serial-number 87 "A" 10) INFO:: Command: (insertion-code-from-serial-number 87 "A" 10) INFO:: Command: (seqnum-from-serial-number 87 "A" 11) INFO:: Command: (insertion-code-from-serial-number 87 "A" 11) INFO:: Command: (seqnum-from-serial-number 87 "A" 12) INFO:: Command: (insertion-code-from-serial-number 87 "A" 12) INFO:: Command: (seqnum-from-serial-number 87 "A" 13) INFO:: Command: (insertion-code-from-serial-number 87 "A" 13) INFO:: Command: (seqnum-from-serial-number 87 "A" 14) INFO:: Command: (insertion-code-from-serial-number 87 "A" 14) INFO:: Command: (seqnum-from-serial-number 87 "A" 15) INFO:: Command: (insertion-code-from-serial-number 87 "A" 15) INFO:: Command: (seqnum-from-serial-number 87 "A" 16) INFO:: Command: (insertion-code-from-serial-number 87 "A" 16) INFO:: Command: (seqnum-from-serial-number 87 "A" 17) INFO:: Command: (insertion-code-from-serial-number 87 "A" 17) INFO:: Command: (seqnum-from-serial-number 87 "A" 18) INFO:: Command: (insertion-code-from-serial-number 87 "A" 18) INFO:: Command: (seqnum-from-serial-number 87 "A" 19) INFO:: Command: (insertion-code-from-serial-number 87 "A" 19) INFO:: Command: (seqnum-from-serial-number 87 "A" 20) INFO:: Command: (insertion-code-from-serial-number 87 "A" 20) INFO:: Command: (seqnum-from-serial-number 87 "A" 21) INFO:: Command: (insertion-code-from-serial-number 87 "A" 21) INFO:: Command: (seqnum-from-serial-number 87 "A" 22) INFO:: Command: (insertion-code-from-serial-number 87 "A" 22) INFO:: Command: (seqnum-from-serial-number 87 "A" 23) INFO:: Command: (insertion-code-from-serial-number 87 "A" 23) INFO:: Command: (seqnum-from-serial-number 87 "A" 24) INFO:: Command: (insertion-code-from-serial-number 87 "A" 24) INFO:: Command: (seqnum-from-serial-number 87 "A" 25) INFO:: Command: (insertion-code-from-serial-number 87 "A" 25) INFO:: Command: (seqnum-from-serial-number 87 "A" 26) INFO:: Command: (insertion-code-from-serial-number 87 "A" 26) INFO:: Command: (seqnum-from-serial-number 87 "A" 27) INFO:: Command: (insertion-code-from-serial-number 87 "A" 27) INFO:: Command: (seqnum-from-serial-number 87 "A" 28) INFO:: Command: (insertion-code-from-serial-number 87 "A" 28) INFO:: Command: (seqnum-from-serial-number 87 "A" 29) INFO:: Command: (insertion-code-from-serial-number 87 "A" 29) INFO:: Command: (seqnum-from-serial-number 87 "A" 30) INFO:: Command: (insertion-code-from-serial-number 87 "A" 30) INFO:: Command: (seqnum-from-serial-number 87 "A" 31) INFO:: Command: (insertion-code-from-serial-number 87 "A" 31) INFO:: Command: (seqnum-from-serial-number 87 "A" 32) INFO:: Command: (insertion-code-from-serial-number 87 "A" 32) INFO:: Command: (seqnum-from-serial-number 87 "A" 33) INFO:: Command: (insertion-code-from-serial-number 87 "A" 33) INFO:: Command: (seqnum-from-serial-number 87 "A" 34) INFO:: Command: (insertion-code-from-serial-number 87 "A" 34) INFO:: Command: (seqnum-from-serial-number 87 "A" 35) INFO:: Command: (insertion-code-from-serial-number 87 "A" 35) INFO:: Command: (seqnum-from-serial-number 87 "A" 36) INFO:: Command: (insertion-code-from-serial-number 87 "A" 36) INFO:: Command: (seqnum-from-serial-number 87 "A" 37) INFO:: Command: (insertion-code-from-serial-number 87 "A" 37) INFO:: Command: (seqnum-from-serial-number 87 "A" 38) INFO:: Command: (insertion-code-from-serial-number 87 "A" 38) INFO:: Command: (seqnum-from-serial-number 87 "A" 39) INFO:: Command: (insertion-code-from-serial-number 87 "A" 39) INFO:: Command: (seqnum-from-serial-number 87 "A" 40) INFO:: Command: (insertion-code-from-serial-number 87 "A" 40) INFO:: Command: (seqnum-from-serial-number 87 "A" 41) INFO:: Command: (insertion-code-from-serial-number 87 "A" 41) INFO:: Command: (seqnum-from-serial-number 87 "A" 42) INFO:: Command: (insertion-code-from-serial-number 87 "A" 42) INFO:: Command: (seqnum-from-serial-number 87 "A" 43) INFO:: Command: (insertion-code-from-serial-number 87 "A" 43) INFO:: Command: (seqnum-from-serial-number 87 "A" 44) INFO:: Command: (insertion-code-from-serial-number 87 "A" 44) INFO:: Command: (seqnum-from-serial-number 87 "A" 45) INFO:: Command: (insertion-code-from-serial-number 87 "A" 45) INFO:: Command: (seqnum-from-serial-number 87 "A" 46) INFO:: Command: (insertion-code-from-serial-number 87 "A" 46) INFO:: Command: (seqnum-from-serial-number 87 "A" 47) INFO:: Command: (insertion-code-from-serial-number 87 "A" 47) INFO:: Command: (seqnum-from-serial-number 87 "A" 48) INFO:: Command: (insertion-code-from-serial-number 87 "A" 48) INFO:: Command: (seqnum-from-serial-number 87 "A" 49) INFO:: Command: (insertion-code-from-serial-number 87 "A" 49) INFO:: Command: (seqnum-from-serial-number 87 "A" 50) INFO:: Command: (insertion-code-from-serial-number 87 "A" 50) INFO:: Command: (seqnum-from-serial-number 87 "A" 51) INFO:: Command: (insertion-code-from-serial-number 87 "A" 51) INFO:: Command: (seqnum-from-serial-number 87 "A" 52) INFO:: Command: (insertion-code-from-serial-number 87 "A" 52) INFO:: Command: (seqnum-from-serial-number 87 "A" 53) INFO:: Command: (insertion-code-from-serial-number 87 "A" 53) INFO:: Command: (seqnum-from-serial-number 87 "A" 54) INFO:: Command: (insertion-code-from-serial-number 87 "A" 54) INFO:: Command: (seqnum-from-serial-number 87 "A" 55) INFO:: Command: (insertion-code-from-serial-number 87 "A" 55) INFO:: Command: (seqnum-from-serial-number 87 "A" 56) INFO:: Command: (insertion-code-from-serial-number 87 "A" 56) INFO:: Command: (seqnum-from-serial-number 87 "A" 57) INFO:: Command: (insertion-code-from-serial-number 87 "A" 57) INFO:: Command: (seqnum-from-serial-number 87 "A" 58) INFO:: Command: (insertion-code-from-serial-number 87 "A" 58) INFO:: Command: (seqnum-from-serial-number 87 "A" 59) INFO:: Command: (insertion-code-from-serial-number 87 "A" 59) INFO:: Command: (seqnum-from-serial-number 87 "A" 60) INFO:: Command: (insertion-code-from-serial-number 87 "A" 60) INFO:: Command: (seqnum-from-serial-number 87 "A" 61) INFO:: Command: (insertion-code-from-serial-number 87 "A" 61) INFO:: Command: (seqnum-from-serial-number 87 "A" 62) INFO:: Command: (insertion-code-from-serial-number 87 "A" 62) INFO:: Command: (seqnum-from-serial-number 87 "A" 63) INFO:: Command: (insertion-code-from-serial-number 87 "A" 63) INFO:: Command: (seqnum-from-serial-number 87 "A" 64) INFO:: Command: (insertion-code-from-serial-number 87 "A" 64) INFO:: Command: (seqnum-from-serial-number 87 "A" 65) INFO:: Command: (insertion-code-from-serial-number 87 "A" 65) INFO:: Command: (seqnum-from-serial-number 87 "A" 66) INFO:: Command: (insertion-code-from-serial-number 87 "A" 66) INFO:: Command: (seqnum-from-serial-number 87 "A" 67) INFO:: Command: (insertion-code-from-serial-number 87 "A" 67) INFO:: Command: (seqnum-from-serial-number 87 "A" 68) INFO:: Command: (insertion-code-from-serial-number 87 "A" 68) INFO:: Command: (seqnum-from-serial-number 87 "A" 69) INFO:: Command: (insertion-code-from-serial-number 87 "A" 69) INFO:: Command: (seqnum-from-serial-number 87 "A" 70) INFO:: Command: (insertion-code-from-serial-number 87 "A" 70) INFO:: Command: (seqnum-from-serial-number 87 "A" 71) INFO:: Command: (insertion-code-from-serial-number 87 "A" 71) INFO:: Command: (seqnum-from-serial-number 87 "A" 72) INFO:: Command: (insertion-code-from-serial-number 87 "A" 72) INFO:: Command: (seqnum-from-serial-number 87 "A" 73) INFO:: Command: (insertion-code-from-serial-number 87 "A" 73) INFO:: Command: (seqnum-from-serial-number 87 "A" 74) INFO:: Command: (insertion-code-from-serial-number 87 "A" 74) INFO:: Command: (seqnum-from-serial-number 87 "A" 75) INFO:: Command: (insertion-code-from-serial-number 87 "A" 75) INFO:: Command: (seqnum-from-serial-number 87 "A" 76) INFO:: Command: (insertion-code-from-serial-number 87 "A" 76) INFO:: Command: (seqnum-from-serial-number 87 "A" 77) INFO:: Command: (insertion-code-from-serial-number 87 "A" 77) INFO:: Command: (seqnum-from-serial-number 87 "A" 78) INFO:: Command: (insertion-code-from-serial-number 87 "A" 78) INFO:: Command: (seqnum-from-serial-number 87 "A" 79) INFO:: Command: (insertion-code-from-serial-number 87 "A" 79) INFO:: Command: (seqnum-from-serial-number 87 "A" 80) INFO:: Command: (insertion-code-from-serial-number 87 "A" 80) INFO:: Command: (seqnum-from-serial-number 87 "A" 81) INFO:: Command: (insertion-code-from-serial-number 87 "A" 81) INFO:: Command: (seqnum-from-serial-number 87 "A" 82) INFO:: Command: (insertion-code-from-serial-number 87 "A" 82) INFO:: Command: (seqnum-from-serial-number 87 "A" 83) INFO:: Command: (insertion-code-from-serial-number 87 "A" 83) INFO:: Command: (seqnum-from-serial-number 87 "A" 84) INFO:: Command: (insertion-code-from-serial-number 87 "A" 84) INFO:: Command: (seqnum-from-serial-number 87 "A" 85) INFO:: Command: (insertion-code-from-serial-number 87 "A" 85) INFO:: Command: (seqnum-from-serial-number 87 "A" 86) INFO:: Command: (insertion-code-from-serial-number 87 "A" 86) INFO:: Command: (seqnum-from-serial-number 87 "A" 87) INFO:: Command: (insertion-code-from-serial-number 87 "A" 87) INFO:: Command: (seqnum-from-serial-number 87 "A" 88) INFO:: Command: (insertion-code-from-serial-number 87 "A" 88) INFO:: Command: (seqnum-from-serial-number 87 "A" 89) INFO:: Command: (insertion-code-from-serial-number 87 "A" 89) INFO:: Command: (seqnum-from-serial-number 87 "A" 90) INFO:: Command: (insertion-code-from-serial-number 87 "A" 90) INFO:: Command: (seqnum-from-serial-number 87 "A" 91) INFO:: Command: (insertion-code-from-serial-number 87 "A" 91) INFO:: Command: (seqnum-from-serial-number 87 "A" 92) INFO:: Command: (insertion-code-from-serial-number 87 "A" 92) INFO:: Command: (seqnum-from-serial-number 87 "B" 0) INFO:: Command: (insertion-code-from-serial-number 87 "B" 0) INFO:: Command: (seqnum-from-serial-number 87 "B" 1) INFO:: Command: (insertion-code-from-serial-number 87 "B" 1) INFO:: Command: (seqnum-from-serial-number 87 "B" 2) INFO:: Command: (insertion-code-from-serial-number 87 "B" 2) INFO:: Command: (seqnum-from-serial-number 87 "B" 3) INFO:: Command: (insertion-code-from-serial-number 87 "B" 3) INFO:: Command: 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(seqnum-from-serial-number 87 "A" 86) INFO:: Command: (insertion-code-from-serial-number 87 "A" 86) INFO:: Command: (seqnum-from-serial-number 87 "A" 87) INFO:: Command: (insertion-code-from-serial-number 87 "A" 87) INFO:: Command: (seqnum-from-serial-number 87 "A" 88) INFO:: Command: (insertion-code-from-serial-number 87 "A" 88) INFO:: Command: (seqnum-from-serial-number 87 "A" 89) INFO:: Command: (insertion-code-from-serial-number 87 "A" 89) INFO:: Command: (seqnum-from-serial-number 87 "A" 90) INFO:: Command: (insertion-code-from-serial-number 87 "A" 90) INFO:: Command: (seqnum-from-serial-number 87 "A" 91) INFO:: Command: (insertion-code-from-serial-number 87 "A" 91) INFO:: Command: (seqnum-from-serial-number 87 "A" 92) INFO:: Command: (insertion-code-from-serial-number 87 "A" 92) INFO:: Command: (seqnum-from-serial-number 87 "B" 0) INFO:: Command: (insertion-code-from-serial-number 87 "B" 0) INFO:: Command: (seqnum-from-serial-number 87 "B" 1) INFO:: Command: (insertion-code-from-serial-number 87 "B" 1) INFO:: Command: (seqnum-from-serial-number 87 "B" 2) INFO:: Command: (insertion-code-from-serial-number 87 "B" 2) INFO:: Command: (seqnum-from-serial-number 87 "B" 3) INFO:: Command: (insertion-code-from-serial-number 87 "B" 3) INFO:: Command: (seqnum-from-serial-number 87 "B" 4) INFO:: Command: (insertion-code-from-serial-number 87 "B" 4) INFO:: Command: (seqnum-from-serial-number 87 "B" 5) INFO:: Command: (insertion-code-from-serial-number 87 "B" 5) INFO:: Command: (seqnum-from-serial-number 87 "B" 6) INFO:: Command: (insertion-code-from-serial-number 87 "B" 6) INFO:: Command: (seqnum-from-serial-number 87 "B" 7) INFO:: Command: (insertion-code-from-serial-number 87 "B" 7) INFO:: Command: (seqnum-from-serial-number 87 "B" 8) INFO:: Command: (insertion-code-from-serial-number 87 "B" 8) INFO:: Command: (seqnum-from-serial-number 87 "B" 9) INFO:: Command: (insertion-code-from-serial-number 87 "B" 9) INFO:: Command: (seqnum-from-serial-number 87 "B" 10) INFO:: Command: (insertion-code-from-serial-number 87 "B" 10) INFO:: Command: (seqnum-from-serial-number 87 "B" 11) INFO:: Command: (insertion-code-from-serial-number 87 "B" 11) INFO:: Command: (seqnum-from-serial-number 87 "B" 12) INFO:: Command: (insertion-code-from-serial-number 87 "B" 12) INFO:: Command: (seqnum-from-serial-number 87 "B" 13) INFO:: Command: (insertion-code-from-serial-number 87 "B" 13) INFO:: Command: (seqnum-from-serial-number 87 "B" 14) INFO:: Command: (insertion-code-from-serial-number 87 "B" 14) INFO:: Command: (seqnum-from-serial-number 87 "B" 15) INFO:: Command: (insertion-code-from-serial-number 87 "B" 15) INFO:: Command: (seqnum-from-serial-number 87 "B" 16) INFO:: Command: (insertion-code-from-serial-number 87 "B" 16) INFO:: Command: (seqnum-from-serial-number 87 "B" 17) INFO:: Command: (insertion-code-from-serial-number 87 "B" 17) INFO:: Command: (seqnum-from-serial-number 87 "B" 18) INFO:: Command: (insertion-code-from-serial-number 87 "B" 18) INFO:: Command: (seqnum-from-serial-number 87 "B" 19) INFO:: Command: (insertion-code-from-serial-number 87 "B" 19) INFO:: Command: (seqnum-from-serial-number 87 "B" 20) INFO:: Command: (insertion-code-from-serial-number 87 "B" 20) INFO:: Command: (seqnum-from-serial-number 87 "B" 21) INFO:: Command: (insertion-code-from-serial-number 87 "B" 21) INFO:: Command: (seqnum-from-serial-number 87 "B" 22) INFO:: Command: (insertion-code-from-serial-number 87 "B" 22) INFO:: Command: (seqnum-from-serial-number 87 "B" 23) INFO:: Command: (insertion-code-from-serial-number 87 "B" 23) INFO:: Command: (seqnum-from-serial-number 87 "B" 24) INFO:: Command: (insertion-code-from-serial-number 87 "B" 24) INFO:: Command: (seqnum-from-serial-number 87 "B" 25) INFO:: Command: (insertion-code-from-serial-number 87 "B" 25) INFO:: Command: (seqnum-from-serial-number 87 "B" 26) INFO:: Command: (insertion-code-from-serial-number 87 "B" 26) INFO:: Command: (seqnum-from-serial-number 87 "B" 27) INFO:: Command: (insertion-code-from-serial-number 87 "B" 27) INFO:: Command: (seqnum-from-serial-number 87 "B" 28) INFO:: Command: (insertion-code-from-serial-number 87 "B" 28) INFO:: Command: (seqnum-from-serial-number 87 "B" 29) INFO:: Command: (insertion-code-from-serial-number 87 "B" 29) INFO:: Command: (seqnum-from-serial-number 87 "B" 30) INFO:: Command: (insertion-code-from-serial-number 87 "B" 30) INFO:: Command: (seqnum-from-serial-number 87 "B" 31) INFO:: Command: (insertion-code-from-serial-number 87 "B" 31) INFO:: Command: (seqnum-from-serial-number 87 "B" 32) INFO:: Command: (insertion-code-from-serial-number 87 "B" 32) INFO:: Command: (seqnum-from-serial-number 87 "B" 33) INFO:: Command: (insertion-code-from-serial-number 87 "B" 33) INFO:: Command: (seqnum-from-serial-number 87 "B" 34) INFO:: Command: (insertion-code-from-serial-number 87 "B" 34) INFO:: Command: (seqnum-from-serial-number 87 "B" 35) INFO:: Command: (insertion-code-from-serial-number 87 "B" 35) INFO:: Command: (seqnum-from-serial-number 87 "B" 36) INFO:: Command: (insertion-code-from-serial-number 87 "B" 36) INFO:: Command: (seqnum-from-serial-number 87 "B" 37) INFO:: Command: (insertion-code-from-serial-number 87 "B" 37) INFO:: Command: (seqnum-from-serial-number 87 "B" 38) INFO:: Command: (insertion-code-from-serial-number 87 "B" 38) INFO:: Command: (seqnum-from-serial-number 87 "B" 39) INFO:: Command: (insertion-code-from-serial-number 87 "B" 39) INFO:: Command: (seqnum-from-serial-number 87 "B" 40) INFO:: Command: (insertion-code-from-serial-number 87 "B" 40) INFO:: Command: (seqnum-from-serial-number 87 "B" 41) INFO:: Command: (insertion-code-from-serial-number 87 "B" 41) INFO:: Command: (seqnum-from-serial-number 87 "B" 42) INFO:: Command: (insertion-code-from-serial-number 87 "B" 42) INFO:: Command: (seqnum-from-serial-number 87 "B" 43) INFO:: Command: (insertion-code-from-serial-number 87 "B" 43) INFO:: Command: (seqnum-from-serial-number 87 "B" 44) INFO:: Command: (insertion-code-from-serial-number 87 "B" 44) INFO:: Command: (seqnum-from-serial-number 87 "B" 45) INFO:: Command: (insertion-code-from-serial-number 87 "B" 45) INFO:: Command: (seqnum-from-serial-number 87 "B" 46) INFO:: Command: (insertion-code-from-serial-number 87 "B" 46) INFO:: Command: (seqnum-from-serial-number 87 "B" 47) INFO:: Command: (insertion-code-from-serial-number 87 "B" 47) INFO:: Command: (seqnum-from-serial-number 87 "B" 48) INFO:: Command: (insertion-code-from-serial-number 87 "B" 48) INFO:: Command: (seqnum-from-serial-number 87 "B" 49) INFO:: Command: (insertion-code-from-serial-number 87 "B" 49) INFO:: Command: (seqnum-from-serial-number 87 "B" 50) INFO:: Command: (insertion-code-from-serial-number 87 "B" 50) INFO:: Command: (seqnum-from-serial-number 87 "B" 51) INFO:: Command: (insertion-code-from-serial-number 87 "B" 51) INFO:: Command: (seqnum-from-serial-number 87 "B" 52) INFO:: Command: (insertion-code-from-serial-number 87 "B" 52) INFO:: Command: (seqnum-from-serial-number 87 "B" 53) INFO:: Command: (insertion-code-from-serial-number 87 "B" 53) INFO:: Command: (seqnum-from-serial-number 87 "B" 54) INFO:: Command: (insertion-code-from-serial-number 87 "B" 54) INFO:: Command: (seqnum-from-serial-number 87 "B" 55) INFO:: Command: (insertion-code-from-serial-number 87 "B" 55) INFO:: Command: (seqnum-from-serial-number 87 "B" 56) INFO:: Command: (insertion-code-from-serial-number 87 "B" 56) INFO:: Command: (seqnum-from-serial-number 87 "B" 57) INFO:: Command: (insertion-code-from-serial-number 87 "B" 57) INFO:: Command: (seqnum-from-serial-number 87 "B" 58) INFO:: Command: (insertion-code-from-serial-number 87 "B" 58) INFO:: Command: (seqnum-from-serial-number 87 "B" 59) INFO:: Command: (insertion-code-from-serial-number 87 "B" 59) INFO:: Command: (seqnum-from-serial-number 87 "B" 60) INFO:: Command: (insertion-code-from-serial-number 87 "B" 60) INFO:: Command: (seqnum-from-serial-number 87 "B" 61) INFO:: Command: (insertion-code-from-serial-number 87 "B" 61) INFO:: Command: (seqnum-from-serial-number 87 "B" 62) INFO:: Command: (insertion-code-from-serial-number 87 "B" 62) INFO:: Command: (seqnum-from-serial-number 87 "B" 63) INFO:: Command: (insertion-code-from-serial-number 87 "B" 63) INFO:: Command: (seqnum-from-serial-number 87 "B" 64) INFO:: Command: (insertion-code-from-serial-number 87 "B" 64) INFO:: Command: (seqnum-from-serial-number 87 "B" 65) INFO:: Command: (insertion-code-from-serial-number 87 "B" 65) INFO:: Command: (seqnum-from-serial-number 87 "B" 66) INFO:: Command: (insertion-code-from-serial-number 87 "B" 66) INFO:: Command: (seqnum-from-serial-number 87 "B" 67) INFO:: Command: (insertion-code-from-serial-number 87 "B" 67) INFO:: Command: (seqnum-from-serial-number 87 "B" 68) INFO:: Command: (insertion-code-from-serial-number 87 "B" 68) INFO:: Command: (seqnum-from-serial-number 87 "B" 69) INFO:: Command: (insertion-code-from-serial-number 87 "B" 69) INFO:: Command: (seqnum-from-serial-number 87 "B" 70) INFO:: Command: (insertion-code-from-serial-number 87 "B" 70) INFO:: Command: (seqnum-from-serial-number 87 "B" 71) INFO:: Command: (insertion-code-from-serial-number 87 "B" 71) INFO:: Command: (seqnum-from-serial-number 87 "B" 72) INFO:: Command: (insertion-code-from-serial-number 87 "B" 72) INFO:: Command: (seqnum-from-serial-number 87 "B" 73) INFO:: Command: (insertion-code-from-serial-number 87 "B" 73) INFO:: Command: (seqnum-from-serial-number 87 "B" 74) INFO:: Command: (insertion-code-from-serial-number 87 "B" 74) INFO:: Command: (seqnum-from-serial-number 87 "B" 75) INFO:: Command: (insertion-code-from-serial-number 87 "B" 75) INFO:: Command: (seqnum-from-serial-number 87 "B" 76) INFO:: Command: (insertion-code-from-serial-number 87 "B" 76) INFO:: Command: (seqnum-from-serial-number 87 "B" 77) INFO:: Command: (insertion-code-from-serial-number 87 "B" 77) INFO:: Command: (seqnum-from-serial-number 87 "B" 78) INFO:: Command: (insertion-code-from-serial-number 87 "B" 78) INFO:: Command: (seqnum-from-serial-number 87 "B" 79) INFO:: Command: (insertion-code-from-serial-number 87 "B" 79) INFO:: Command: (seqnum-from-serial-number 87 "B" 80) INFO:: Command: (insertion-code-from-serial-number 87 "B" 80) INFO:: Command: (seqnum-from-serial-number 87 "B" 81) INFO:: Command: (insertion-code-from-serial-number 87 "B" 81) INFO:: Command: (seqnum-from-serial-number 87 "B" 82) INFO:: Command: (insertion-code-from-serial-number 87 "B" 82) INFO:: Command: (seqnum-from-serial-number 87 "B" 83) INFO:: Command: (insertion-code-from-serial-number 87 "B" 83) INFO:: Command: (seqnum-from-serial-number 87 "B" 84) INFO:: Command: (insertion-code-from-serial-number 87 "B" 84) INFO:: Command: (seqnum-from-serial-number 87 "B" 85) INFO:: Command: (insertion-code-from-serial-number 87 "B" 85) INFO:: Command: (seqnum-from-serial-number 87 "B" 86) INFO:: Command: (insertion-code-from-serial-number 87 "B" 86) INFO:: Command: (seqnum-from-serial-number 87 "B" 87) INFO:: Command: (insertion-code-from-serial-number 87 "B" 87) INFO:: Command: (seqnum-from-serial-number 87 "B" 88) INFO:: Command: (insertion-code-from-serial-number 87 "B" 88) INFO:: Command: (seqnum-from-serial-number 87 "B" 89) INFO:: Command: (insertion-code-from-serial-number 87 "B" 89) INFO:: Command: (seqnum-from-serial-number 87 "B" 90) INFO:: Command: (insertion-code-from-serial-number 87 "B" 90) INFO:: Command: (seqnum-from-serial-number 87 "B" 91) INFO:: Command: (insertion-code-from-serial-number 87 "B" 91) INFO:: Command: (seqnum-from-serial-number 87 "B" 92) INFO:: Command: (insertion-code-from-serial-number 87 "B" 92) INFO:: Command: (seqnum-from-serial-number 87 "B" 93) INFO:: Command: (insertion-code-from-serial-number 87 "B" 93) INFO:: Command: (seqnum-from-serial-number 87 "B" 94) INFO:: Command: (insertion-code-from-serial-number 87 "B" 94) INFO:: Command: (seqnum-from-serial-number 87 "B" 95) INFO:: Command: (insertion-code-from-serial-number 87 "B" 95) 0 [87, 'A', 1, ''] 1 [87, 'A', 2, ''] 2 [87, 'A', 3, ''] 3 [87, 'A', 4, ''] 4 [87, 'A', 5, ''] 5 [87, 'A', 6, ''] 6 [87, 'A', 7, ''] 7 [87, 'A', 8, ''] 8 [87, 'A', 9, ''] 9 [87, 'A', 10, ''] 10 [87, 'A', 11, ''] 11 [87, 'A', 12, ''] 12 [87, 'A', 13, ''] 13 [87, 'A', 14, ''] 14 [87, 'A', 15, ''] 15 [87, 'A', 16, ''] 16 [87, 'A', 17, ''] 17 [87, 'A', 18, ''] 18 [87, 'A', 19, ''] 19 [87, 'A', 20, ''] 20 [87, 'A', 21, ''] 21 [87, 'A', 22, ''] 22 [87, 'A', 23, ''] 23 [87, 'A', 24, ''] 24 [87, 'A', 25, ''] 25 [87, 'A', 26, ''] 26 [87, 'A', 27, ''] 27 [87, 'A', 28, ''] 28 [87, 'A', 29, ''] 29 [87, 'A', 30, ''] 30 [87, 'A', 31, ''] 31 [87, 'A', 32, ''] 32 [87, 'A', 33, ''] 33 [87, 'A', 34, ''] 34 [87, 'A', 35, ''] 35 [87, 'A', 36, ''] 36 [87, 'A', 37, ''] 36 [87, 'A', 37, ''] 37 [87, 'A', 38, ''] 38 [87, 'A', 39, ''] 39 [87, 'A', 40, ''] 40 [87, 'A', 41, ''] 41 [87, 'A', 42, ''] 42 [87, 'A', 43, ''] 43 [87, 'A', 44, ''] 44 [87, 'A', 45, ''] 45 [87, 'A', 46, ''] 46 [87, 'A', 47, ''] 47 [87, 'A', 48, ''] 48 [87, 'A', 49, ''] 49 [87, 'A', 50, ''] 50 [87, 'A', 51, ''] 51 [87, 'A', 52, ''] 52 [87, 'A', 53, ''] 53 [87, 'A', 54, ''] 54 [87, 'A', 55, ''] 55 [87, 'A', 56, ''] 56 [87, 'A', 57, ''] 57 [87, 'A', 58, ''] 58 [87, 'A', 59, ''] 59 [87, 'A', 60, ''] 60 [87, 'A', 61, ''] 61 [87, 'A', 62, ''] 62 [87, 'A', 63, ''] 63 [87, 'A', 64, ''] 64 [87, 'A', 65, ''] 65 [87, 'A', 66, ''] 66 [87, 'A', 67, ''] 67 [87, 'A', 68, ''] 68 [87, 'A', 69, ''] 69 [87, 'A', 70, ''] 70 [87, 'A', 71, ''] 71 [87, 'A', 72, ''] 72 [87, 'A', 73, ''] 73 [87, 'A', 74, ''] 74 [87, 'A', 75, ''] 75 [87, 'A', 76, ''] 76 [87, 'A', 77, ''] 77 [87, 'A', 78, ''] 78 [87, 'A', 79, ''] 79 [87, 'A', 80, ''] 80 [87, 'A', 81, ''] 81 [87, 'A', 82, ''] 82 [87, 'A', 83, ''] 83 [87, 'A', 84, ''] 84 [87, 'A', 85, ''] 85 [87, 'A', 86, ''] 86 [87, 'A', 87, ''] 87 [87, 'A', 88, ''] 88 [87, 'A', 89, ''] 89 [87, 'A', 90, ''] 90 [87, 'A', 91, ''] 91 [87, 'A', 92, ''] 92 [87, 'A', 93, ''] 93 [87, 'B', 1, ''] 94 [87, 'B', 2, ''] 95 [87, 'B', 3, ''] 96 [87, 'B', 4, ''] 97 [87, 'B', 5, ''] 98 [87, 'B', 6, ''] 99 [87, 'B', 7, ''] 100 [87, 'B', 8, ''] 101 [87, 'B', 9, ''] 102 [87, 'B', 10, ''] 103 [87, 'B', 11, ''] 104 [87, 'B', 12, ''] 105 [87, 'B', 13, ''] 106 [87, 'B', 14, ''] 107 [87, 'B', 15, ''] 108 [87, 'B', 16, ''] 109 [87, 'B', 17, ''] 110 [87, 'B', 18, ''] 111 [87, 'B', 19, ''] 112 [87, 'B', 20, ''] 113 [87, 'B', 21, ''] 114 [87, 'B', 22, ''] 115 [87, 'B', 23, ''] 116 [87, 'B', 24, ''] 117 [87, 'B', 25, ''] 118 [87, 'B', 26, ''] 119 [87, 'B', 27, ''] 120 [87, 'B', 28, ''] 121 [87, 'B', 29, ''] 122 [87, 'B', 30, ''] 123 [87, 'B', 31, ''] 124 [87, 'B', 32, ''] 125 [87, 'B', 33, ''] 126 [87, 'B', 34, ''] 127 [87, 'B', 35, ''] 128 [87, 'B', 36, ''] 129 [87, 'B', 37, ''] 130 [87, 'B', 38, ''] 131 [87, 'B', 39, ''] 132 [87, 'B', 40, ''] 133 [87, 'B', 41, ''] 134 [87, 'B', 42, ''] 135 [87, 'B', 43, ''] 136 [87, 'B', 44, ''] 137 [87, 'B', 45, ''] 138 [87, 'B', 46, ''] 139 [87, 'B', 47, ''] 140 [87, 'B', 48, ''] 141 [87, 'B', 49, ''] 142 [87, 'B', 50, ''] 143 [87, 'B', 51, ''] 144 [87, 'B', 52, ''] 145 [87, 'B', 53, ''] 146 [87, 'B', 54, ''] 147 [87, 'B', 55, ''] 148 [87, 'B', 56, ''] 149 [87, 'B', 57, ''] 150 [87, 'B', 58, ''] 151 [87, 'B', 59, ''] 152 [87, 'B', 60, ''] 153 [87, 'B', 61, ''] 154 [87, 'B', 62, ''] 155 [87, 'B', 63, ''] 156 [87, 'B', 64, ''] 157 [87, 'B', 65, ''] 158 [87, 'B', 66, ''] 159 [87, 'B', 67, ''] 160 [87, 'B', 68, ''] 161 [87, 'B', 69, ''] 162 [87, 'B', 70, ''] 163 [87, 'B', 71, ''] 164 [87, 'B', 72, ''] 165 [87, 'B', 73, ''] 166 [87, 'B', 74, ''] 167 [87, 'B', 75, ''] 168 [87, 'B', 76, ''] 169 [87, 'B', 77, ''] 170 [87, 'B', 78, ''] 171 [87, 'B', 79, ''] 172 [87, 'B', 80, ''] 173 [87, 'B', 81, ''] 174 [87, 'B', 82, ''] 175 [87, 'B', 83, ''] 176 [87, 'B', 84, ''] 177 [87, 'B', 85, ''] 178 [87, 'B', 86, ''] 179 [87, 'B', 87, ''] 180 [87, 'B', 88, ''] 181 [87, 'B', 89, ''] 182 [87, 'B', 90, ''] 183 [87, 'B', 91, ''] 184 [87, 'B', 92, ''] 185 [87, 'B', 93, ''] 186 [87, 'B', 94, ''] 187 [87, 'B', 95, ''] 188 [87, 'B', 96, ''] ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 88 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (n-chains 88) INFO:: Command: (chain_id 88 0) INFO:: Command: (chain_id 88 1) INFO:: Command: (seqnum-from-serial-number 88 "A" 0) INFO:: Command: (insertion-code-from-serial-number 88 "A" 0) INFO:: Command: (seqnum-from-serial-number 88 "A" 1) INFO:: Command: (insertion-code-from-serial-number 88 "A" 1) INFO:: Command: (seqnum-from-serial-number 88 "A" 2) INFO:: Command: (insertion-code-from-serial-number 88 "A" 2) INFO:: Command: (seqnum-from-serial-number 88 "A" 3) INFO:: Command: (insertion-code-from-serial-number 88 "A" 3) INFO:: Command: (seqnum-from-serial-number 88 "A" 4) INFO:: Command: (insertion-code-from-serial-number 88 "A" 4) INFO:: Command: (seqnum-from-serial-number 88 "A" 5) INFO:: Command: (insertion-code-from-serial-number 88 "A" 5) INFO:: Command: (seqnum-from-serial-number 88 "A" 6) INFO:: Command: (insertion-code-from-serial-number 88 "A" 6) INFO:: Command: (seqnum-from-serial-number 88 "A" 7) INFO:: Command: (insertion-code-from-serial-number 88 "A" 7) INFO:: Command: (seqnum-from-serial-number 88 "A" 8) INFO:: Command: (insertion-code-from-serial-number 88 "A" 8) INFO:: Command: (seqnum-from-serial-number 88 "A" 9) INFO:: Command: (insertion-code-from-serial-number 88 "A" 9) INFO:: Command: (seqnum-from-serial-number 88 "A" 10) INFO:: Command: (insertion-code-from-serial-number 88 "A" 10) INFO:: Command: (seqnum-from-serial-number 88 "A" 11) INFO:: Command: (insertion-code-from-serial-number 88 "A" 11) INFO:: Command: (seqnum-from-serial-number 88 "A" 12) INFO:: Command: (insertion-code-from-serial-number 88 "A" 12) INFO:: Command: (seqnum-from-serial-number 88 "A" 13) INFO:: Command: (insertion-code-from-serial-number 88 "A" 13) INFO:: Command: (seqnum-from-serial-number 88 "A" 14) INFO:: Command: (insertion-code-from-serial-number 88 "A" 14) INFO:: Command: (seqnum-from-serial-number 88 "A" 15) INFO:: Command: (insertion-code-from-serial-number 88 "A" 15) INFO:: Command: (seqnum-from-serial-number 88 "A" 16) INFO:: Command: (insertion-code-from-serial-number 88 "A" 16) INFO:: Command: (seqnum-from-serial-number 88 "A" 17) INFO:: Command: (insertion-code-from-serial-number 88 "A" 17) INFO:: Command: (seqnum-from-serial-number 88 "A" 18) INFO:: Command: (insertion-code-from-serial-number 88 "A" 18) INFO:: Command: (seqnum-from-serial-number 88 "A" 19) INFO:: Command: (insertion-code-from-serial-number 88 "A" 19) INFO:: Command: (seqnum-from-serial-number 88 "A" 20) INFO:: Command: (insertion-code-from-serial-number 88 "A" 20) INFO:: Command: (seqnum-from-serial-number 88 "A" 21) INFO:: Command: (insertion-code-from-serial-number 88 "A" 21) INFO:: Command: 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[88, 'B', 33, ''], [88, 'B', 34, ''], [88, 'B', 35, ''], [88, 'B', 36, ''], [88, 'B', 37, ''], [88, 'B', 38, ''], [88, 'B', 39, ''], [88, 'B', 40, ''], [88, 'B', 41, ''], [88, 'B', 42, ''], [88, 'B', 43, ''], [88, 'B', 44, ''], [88, 'B', 45, ''], [88, 'B', 46, ''], [88, 'B', 47, ''], [88, 'B', 48, ''], [88, 'B', 49, ''], [88, 'B', 50, ''], [88, 'B', 51, ''], [88, 'B', 52, ''], [88, 'B', 53, ''], [88, 'B', 54, ''], [88, 'B', 55, ''], [88, 'B', 56, ''], [88, 'B', 57, ''], [88, 'B', 58, ''], [88, 'B', 59, ''], [88, 'B', 60, ''], [88, 'B', 61, ''], [88, 'B', 62, ''], [88, 'B', 63, ''], [88, 'B', 64, ''], [88, 'B', 65, ''], [88, 'B', 66, ''], [88, 'B', 67, ''], [88, 'B', 68, ''], [88, 'B', 69, ''], [88, 'B', 70, ''], [88, 'B', 71, ''], [88, 'B', 72, ''], [88, 'B', 73, ''], [88, 'B', 74, ''], [88, 'B', 75, ''], [88, 'B', 76, ''], [88, 'B', 77, ''], [88, 'B', 78, ''], [88, 'B', 79, ''], [88, 'B', 80, ''], [88, 'B', 81, ''], [88, 'B', 82, ''], [88, 'B', 83, ''], [88, 'B', 84, ''], [88, 'B', 85, ''], [88, 'B', 86, ''], [88, 'B', 87, ''], [88, 'B', 88, ''], [88, 'B', 89, ''], [88, 'B', 90, ''], [88, 'B', 91, ''], [88, 'B', 92, ''], [88, 'B', 93, ''], [88, 'B', 94, ''], [88, 'B', 95, ''], [88, 'B', 96, '']] ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2goz-manip.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2goz-manip.pdb PDB file /home/paule/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 10/85 Molecule 89 read successfully DEBUG:: there were 7 types with no dictionary ok test60_0 (__main__.PdbMtzTestFunctions) post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok test61_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... INFO:: Command: (write-pdb-file 0 "rnase_zip_test.pdb.gz") INFO:: Command: (handle-read-draw-molecule-with-recentre "rnase_zip_test.pdb.gz" 1) gzip: stdout: Broken pipe gzip: stdout: Broken pipe INFO:: Reading coordinate file: rnase_zip_test.pdb.gz PDB file rnase_zip_test.pdb.gz has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 90 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 2 CB ok test62_0 (__main__.PdbMtzTestFunctions) Fix for Oliver Clarke fit by atom selection bug ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 91 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.023 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.04051e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.014 seconds for contour map INFO:: 0.057 seconds in total masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:45:06_2018_modification_0.pdb.gz INFO:: replace_coords: 745 atoms updated. bl: 0.0363730669589 ok test999_0 (__main__.PdbMtzTestFunctions) Renumber residue range without overwriting coordinates. ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 93 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_23:45:06_2018_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 93 "A" 10 20 -55) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:45:06_2018_modification_1.pdb.gz INFO:: Command: (renumber-residue-range 93 "A" 90 93 10) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:45:06_2018_modification_2.pdb.gz INFO:: Command: (renumber-residue-range 93 "A" 89 91 1) WARNING:: the new residue range overlaps with original one. Please change the range. Nothing has been done. INFO:: Command: (renumber-residue-range 93 "A" 80 91 12) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:45:06_2018_modification_3.pdb.gz INFO:: Command: (renumber-residue-range 93 "A" -100 200 9) ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/HOF.RES" 1) SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.9028 13.6977 9.2374 90 98.211 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 INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/HOF.RES") ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/hollander.ins" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.3243 34.3243 11.0887 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:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/hollander.ins") INFO:: spacegroup: I 41 2 2 ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.726 77.726 77.726 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 INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/insulin.res") Map statistics: mean: -5.07007e-05 st.d: 0.305174 Map statistics: min: -0.781031, max: 6.07907 -0.69528 231 -0.523777 4724 -0.352275 24910 -0.180772 55291 -0.00926974 95241 0.162233 40930 0.333735 7480 0.505238 3968 0.67674 2790 0.848243 2117 1.01975 1738 1.19125 1221 1.36275 888 1.53425 595 1.70576 355 1.87726 240 2.04876 137 2.22026 97 2.39177 62 2.56327 46 2.73477 17 2.90627 17 3.07778 13 3.24928 10 3.42078 7 3.59228 1 3.76379 3 3.93529 7 4.10679 2 4.27829 5 4.4498 1 4.6213 2 4.7928 2 4.9643 0 5.13581 1 5.30731 0 5.47881 0 5.65031 0 5.82182 0 5.99332 0 6.16482 1 Map statistics: mean: -1.00548e-05 st.d: 0.0468085 Map statistics: min: -0.211523, max: 0.648623 -0.200772 7 -0.179268 48 -0.157764 209 -0.136261 787 -0.114757 2257 -0.0932533 5676 -0.0717496 12730 -0.050246 24380 -0.0287423 38191 -0.00723865 46229 0.014265 43880 0.0357687 32484 0.0572724 19420 0.078776 9718 0.10028 4120 0.121783 1677 0.143287 718 0.164791 329 0.186294 133 0.207798 77 0.229302 29 0.250805 11 0.272309 13 0.293813 8 0.315316 2 0.33682 2 0.358324 2 0.379827 1 0.401331 1 0.422835 2 0.444338 2 0.465842 1 0.487346 1 0.508849 1 0.530353 1 0.551857 1 0.57336 0 0.594864 0 0.616368 0 0.637871 2 0.659375 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... WARNING:: invalid molecule (204050) for write_shelx_ins_file WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... INFO:: Command: (update-go-to-atom-window-on-new-mol) ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... INFO:: Command: (update-go-to-atom-window-on-new-mol) fitting terminal residue with 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_23:45:07_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:: Command: (add-terminal-residue 100 "B" 2020 1) ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... INFO:: Command: (set-rotation-centre 3.00 -1.00 60.00) INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Tue_Jan__2_23:45:07_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:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (resname-from-serial-number 96 "D" 68) INFO:: Command: (seqnum-from-serial-number 96 "D" 68) INFO:: Command: (insertion-code-from-serial-number 96 "D" 68) ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... INFO:: Command: (n-chains 96) 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 0.305174 INFO:: Using density cut-off: 0.183104 (0.6 sigma) (mean -0.0203497 stdev: 0.111926) 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_23:45:07_2018_modification_1.res WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C " WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB " WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1" WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1" INFO:: Adding to solvent chain: D INFO:: Command: (n-chains 96) INFO:: Command: (resname-from-serial-number 96 "D" 96) INFO:: Command: (seqnum-from-serial-number 96 "D" 96) INFO:: Command: (insertion-code-from-serial-number 96 "D" 96) ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/miller/shelx-test4-NPD-mini.res" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.14 83.03 89.79 90 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 INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/miller/shelx-test4-NPD-mini.res") INFO:: Command: (close-molecule 101) ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... INFO:: Command: (close-molecule 97) INFO:: Command: (close-molecule 96) ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/horma-p21.res" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.73 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 INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/horma-p21.res") WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " O1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C2 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H3 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H4 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C5 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" "CL1 " WARNING:: failed to get AFIX handle for "A" 1 "CPC" " N1 " INFO:: SHELXL file new-horma.ins written. INFO:: Command: (handle-read-draw-molecule-with-recentre "new-horma.ins" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL debug:: ## new chain wiith chain-id A INFO:: CELL set to 14.08 32.76 18.66 90 101.73 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 INFO:: Command: (read-shelx-ins-file "new-horma.ins") b_1: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] b_2: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/crash.hat" 0) LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.999 108.999 107.555 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:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/crash.hat") INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/crash.hat" 1) LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.999 108.999 107.555 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 105 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/crash.hat") ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 0) INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb PDB file coot-ccp4/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 106 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:45:08_2018_modification_0.pdb.gz Welcome to Coot INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:45:08_2018_modification_1.pdb.gz INFO:: Command: (delete-residue-hydrogens 106 "A" 1 "" "") ok test02_0 (__main__.LigandTestFunctions) Set Bond thickness test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-3GP.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 107 read successfully DEBUG:: there were 0 types with no dictionary here 1 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Tue_Jan__2_23:45:08_2018_modification_0.pdb.gz ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/test-LIG.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb PDB file /home/paule/data/greg-data/test-LIG.pdb has been read. 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:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/test-LIG.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb PDB file /home/paule/data/greg-data/test-LIG.pdb has been read. 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 109 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary ok test05_0 (__main__.LigandTestFunctions) Move and Refine Ligand test ... INFO:: Command: (go-to-view-number 2 1) INFO:: Command: (set-rotation-centre 55.30 9.10 20.60) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:45:08_2018_modification_2.pdb.gz INFO:: Command: (backup-state 106) INFO:: Command: (turn-off-backup 106) ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Command: (turn-on-backup 106) ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/monomer-NPO.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices Molecule 110 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (copy-molecule 110) INFO:: Command: (copy-molecule 110) INFO:: Command: (copy-molecule 110) INFO:: Command: (copy-molecule 110) INFO:: Command: (copy-molecule 110) INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 0/113 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 0/117 INFO:: fill_ghost_info Constructed 6 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain A" Ghost 1 name: "NCS found from matching Chain E onto Chain A" Ghost 2 name: "NCS found from matching Chain G onto Chain A" Ghost 3 name: "NCS found from matching Chain D onto Chain B" Ghost 4 name: "NCS found from matching Chain F onto Chain B" Ghost 5 name: "NCS found from matching Chain H onto Chain B" Molecule 116 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:: 0.13 seconds to read MTZ file INFO:: 0.093 seconds to initialize map INFO:: 0.072 seconds for FFT INFO:: 0.013 seconds for statistics Map mean: ........ -8.79014e-07 Map sigma: ....... 0.171188 Map maximum: ..... 1.34304 Map minimum: ..... -0.695441 INFO:: 0.006 seconds for contour map INFO:: 0.314 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: making difference map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT Number of OBSERVED reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.072 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.071 seconds for FFT INFO:: 0.013 seconds for statistics Map mean: ........ 2.09389e-06 Map sigma: ....... 0.0333923 Map maximum: ..... 0.366077 Map minimum: ..... -0.191665 INFO:: 0.003 seconds for contour map INFO:: 0.161 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "DELFWT" "PHDELWT" "" 0 1 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: ligand number 0 is molecule number 110 with wiggly flag: 0 in execute_ligand_search_internal() import maps from mol 117 INFO:: Protein centre at: xyz = ( 58.29, 34.65, 30.63) Map statistics: mean: -0.0216745 st.d: 0.0886263 Map statistics: min: -0.695441, max: 0.754209 -0.67732 6 -0.641079 8 -0.604838 27 -0.568596 116 -0.532355 354 -0.496114 977 -0.459873 1943 -0.423631 3356 -0.38739 5156 -0.351149 6576 -0.314908 7850 -0.278666 8875 -0.242425 9742 -0.206184 11742 -0.169943 16950 -0.133701 29805 -0.0974601 58214 -0.0612189 102889 -0.0249776 142998 0.0112636 471776 0.0475049 106846 0.0837461 56087 0.119987 21597 0.156229 6911 0.19247 2135 0.228711 920 0.264952 467 0.301194 346 0.337435 216 0.373676 118 0.409917 117 0.446159 80 0.4824 50 0.518641 28 0.554882 33 0.591124 15 0.627365 14 0.663606 11 0.699847 2 0.736089 7 0.77233 0 INFO:: find_clusters map_rms is 0.171132 INFO:: Using density cut-off: 0.171132 (1 sigma) (mean -0.0216776 stdev: 0.0886191) 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 4.04204 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 2.01801 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 2.09013 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 1.85884 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 1.39127 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 1.68437 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 2.09611 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 1.63625 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 2.07009 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 1.85739 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 Fitting NPO gave these results: [120, 121, 122, 123, 124, 125, 126, 127, 128, 129] ok test07_0 (__main__.LigandTestFunctions) Flip residue (around eigen vectors) ... INFO:: Command: (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 1) 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 130 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (copy-molecule 130) INFO:: Command: (set-go-to-atom-molecule 130) INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:45:19_2018_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. distance: 4.35071923863 INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Jan__2_23:45:19_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_23:45:19_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_23:45:19_2018_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. distance d2: 8.6494937029e-08 ok test08_0 (__main__.LigandTestFunctions) Test dipole ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/dipole-residues.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/dipole-residues.pdb PDB file /home/paule/data/greg-data/dipole-residues.pdb has been read. 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 132 read successfully DEBUG:: there were 0 types with no dictionary info:: dipole components [-2.219999939203263, 4.440892098500626e-16, 0.0] ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints ok test10_0 (__main__.LigandTestFunctions) Pyrogen Runs OK? ... ok test11_0 (__main__.LigandTestFunctions) pyrogen dictionary does not make double-quoted atom names ... ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 133 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 133 INFO:: Command: (assign-pir-sequence 133 "A" ">test ACDEFGHIKLMNPQ*") debug seq ACDEFGHIKLMNPQ storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 133 INFO:: Command: (assign-pir-sequence 133 "A" ">test ACDEFGHIKLMNPQRST*") ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb PDB file /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 134 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 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: ........ 1.04051e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.013 seconds for contour map INFO:: 0.057 seconds in total storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 134 INFO:: Command: (assign-pir-sequence 134 "A" "> tutorial-modern chain A RNASE DVSGTVCLSA LPPEATDTLN LIASDGPFPY SQDGVVFQNR ESVLPTQSYG YYHEYTVITP GARTRGTRRI ICGEATQEDY YTGDHYATFS LID * ") INFO:: Command: (set-rotation-centre 64.27 7.04 14.42) Cootaneering: imol 134 chain-id B resno 60 inscode at-name CA alt-conf Sequence: ?EYTVITPGARTR Confidence: 0.999999 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_23:45:22_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. ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 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_23:45:23_2018_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 0/8 INFO:: Command: (copy-molecule 136) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 76.27 10.04 14.42) INFO:: Command: (go-to-view-number 3 1) INFO:: Command: (n-chains 137) INFO:: Command: (chain_id 137 0) INFO:: Command: (chain_id 137 1) INFO:: Command: (is-solvent-chain-p 137 "A") There are 8 residues in chain A INFO:: Command: (resname-from-serial-number 137 "A" 0) INFO:: Command: (seqnum-from-serial-number 137 "A" 0) INFO:: Command: (insertion-code-from-serial-number 137 "A" 0) INFO:: Command: (resname-from-serial-number 137 "A" 1) INFO:: Command: (seqnum-from-serial-number 137 "A" 1) INFO:: Command: (insertion-code-from-serial-number 137 "A" 1) INFO:: Command: (resname-from-serial-number 137 "A" 2) INFO:: Command: (seqnum-from-serial-number 137 "A" 2) INFO:: Command: (insertion-code-from-serial-number 137 "A" 2) INFO:: Command: (resname-from-serial-number 137 "A" 3) INFO:: Command: (seqnum-from-serial-number 137 "A" 3) INFO:: Command: (insertion-code-from-serial-number 137 "A" 3) INFO:: Command: (resname-from-serial-number 137 "A" 4) INFO:: Command: (seqnum-from-serial-number 137 "A" 4) INFO:: Command: (insertion-code-from-serial-number 137 "A" 4) INFO:: Command: (resname-from-serial-number 137 "A" 5) INFO:: Command: (seqnum-from-serial-number 137 "A" 5) INFO:: Command: (insertion-code-from-serial-number 137 "A" 5) INFO:: Command: (resname-from-serial-number 137 "A" 6) INFO:: Command: (seqnum-from-serial-number 137 "A" 6) INFO:: Command: (insertion-code-from-serial-number 137 "A" 6) INFO:: Command: (resname-from-serial-number 137 "A" 7) INFO:: Command: (seqnum-from-serial-number 137 "A" 7) INFO:: Command: (insertion-code-from-serial-number 137 "A" 7) INFO:: Command: (is-solvent-chain-p 137 "B") There are 8 residues in chain B INFO:: Command: (resname-from-serial-number 137 "B" 0) INFO:: Command: (seqnum-from-serial-number 137 "B" 0) INFO:: Command: (insertion-code-from-serial-number 137 "B" 0) INFO:: Command: (resname-from-serial-number 137 "B" 1) INFO:: Command: (seqnum-from-serial-number 137 "B" 1) INFO:: Command: (insertion-code-from-serial-number 137 "B" 1) INFO:: Command: (resname-from-serial-number 137 "B" 2) INFO:: Command: (seqnum-from-serial-number 137 "B" 2) INFO:: Command: (insertion-code-from-serial-number 137 "B" 2) INFO:: Command: (resname-from-serial-number 137 "B" 3) INFO:: Command: (seqnum-from-serial-number 137 "B" 3) INFO:: Command: (insertion-code-from-serial-number 137 "B" 3) INFO:: Command: (resname-from-serial-number 137 "B" 4) INFO:: Command: (seqnum-from-serial-number 137 "B" 4) INFO:: Command: (insertion-code-from-serial-number 137 "B" 4) INFO:: Command: (resname-from-serial-number 137 "B" 5) INFO:: Command: (seqnum-from-serial-number 137 "B" 5) INFO:: Command: (insertion-code-from-serial-number 137 "B" 5) INFO:: Command: (resname-from-serial-number 137 "B" 6) INFO:: Command: (seqnum-from-serial-number 137 "B" 6) INFO:: Command: (insertion-code-from-serial-number 137 "B" 6) INFO:: Command: (resname-from-serial-number 137 "B" 7) INFO:: Command: (seqnum-from-serial-number 137 "B" 7) INFO:: Command: (insertion-code-from-serial-number 137 "B" 7) 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: (67.803,-2.64114,8.31226) B-factor: 76.88 First atom of 170 in second selection 1/C/1 {G}/ P altLoc :: segid :: pos: (91.8051,21.361,32.3144) B-factor: 76.88 INFO:: LSQ matched 8 atoms INFO:: 8 matched atoms had: mean devi: 2.15081e-06 rms devi: 2.21606e-06 max devi: 3.03293e-06 min devi: 1.50221e-06 find_ncs_matrix returns (LSQ) | 1,-5.212e-08, 1.588e-07| | 5.212e-08, 1,-1.752e-08| |-1.588e-07, 1.752e-08, 1| ( -24, -24, -24) 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: (69.1889,-2.00913,20.5443) B-factor: 76.88 First atom of 170 in second selection 1/D/1 {C}/ P altLoc :: segid :: pos: (93.191,21.993,44.5464) B-factor: 76.88 INFO:: LSQ matched 8 atoms INFO:: 8 matched atoms had: mean devi: 1.20632e-06 rms devi: 1.2589e-06 max devi: 1.73211e-06 min devi: 6.41607e-07 find_ncs_matrix returns (LSQ) | 1, 6.798e-08, 5.219e-08| |-6.798e-08, 1, 5.633e-09| |-5.219e-08,-5.633e-09, 1| ( -24, -24, -24) 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:: Command: (copy-molecule 136) INFO:: Matching/moving molecule number 138 to 138 INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 2.32672e-06 rms devi: 2.52357e-06 max devi: 4.12857e-06 min devi: 2.38099e-07 INFO:: Axis orientation: ( 0.3652, -0.5575, 0.7455) INFO:: Rotation in CCP4 Polar Angles: Polar = ( 0, 0, 0) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Tue_Jan__2_23:45:23_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 1, 2.189e-08, 1.637e-08| |-2.189e-08, 1, 1.073e-08| |-1.637e-08,-1.073e-08, 1| ( -24, -24, -24) No unit cell for this molecule, hence no fractional matrix. INFO:: Command: (go-to-view-number 4 1) ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/1wly.pdb" 0) INFO:: Reading coordinate file: /home/paule/data/greg-data/1wly.pdb PDB file /home/paule/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 139 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/1yb5.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/1yb5.pdb PDB file /home/paule/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 324/324 INFO:: NCS chain comparison 0/324 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 140 read successfully DEBUG:: there were 2 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: Command: (graphics-to-ca-plus-ligands-representation 139) INFO:: Command: (graphics-to-ca-plus-ligands-representation 140) INFO:: reference 139 has 750 atoms selected INFO:: moving 140 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_23:45:24_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.9117, -0.3803, 0.1557| | -0.3625, 0.9227, 0.131| | -0.1935, 0.06299, -0.9791| ( 70.65, 7.793, 21.29) Rotation - polar (omega,phi,kappa) 87.1413 101.0220 169.7385 Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277 Translation - Angstroms 70.6538 7.7930 21.2852 INFO: core rmsd achieved: 1.0199 Angstroems number of residues in reference structure: 322 number of residues in moving structure: 324 number of residues in aligned sections (reference): 100 number of residues in aligned sections (moving): 110 number of aligned residues: 95 number of gaps: 4 number of misdirections: 0 number of SSE combinations: 4.0000 sequence identity: 30.5263% INFO:: Command: (set-rotation-centre 65.65 -3.00 -4.00) INFO:: Command: (go-to-view-number 5 1) ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/1pyd.pdb" 0) WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb INFO:: Command: (graphics-to-ca-plus-ligands-representation -1) INFO:: Command: (set-graphics-window-size 678 452) INFO:: Command: (molecule-name 0) 0 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 1) 1 /home/paule/data/greg-data/ins-code-fragment-pre.pdb 2 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 3 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 4) 4 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 5) 5 mainchain INFO:: Command: (molecule-name 6) 6 /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: Command: (molecule-name 7) 7 regression-test-terminal-residue.pdb INFO:: Command: (molecule-name 8) 8 atom selection from regression-test-terminal-residue.pdb INFO:: Command: (molecule-name 9) 9 /home/paule/data/greg-data/frag-2wot.pdb INFO:: Command: (molecule-name 10) 10 sphere selection from tutorial-modern.pdb INFO:: Command: (molecule-name 11) 11 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 13) 13 /home/paule/data/greg-data/rotamer-test-fragment.pdb INFO:: Command: (molecule-name 14) 14 /home/paule/data/greg-data/res098.pdb INFO:: Command: (molecule-name 15) 15 /home/paule/data/greg-data/tutorial-modern.pdb 16 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 17) 17 /home/paule/data/greg-data/pdb3knw.ent INFO:: Command: (molecule-name 18) 18 /home/paule/data/greg-data/pdb1py3.ent INFO:: Command: (molecule-name 21) 21 /home/paule/data/greg-data/alt-conf-pepflip-test.pdb INFO:: Command: (molecule-name 22) 22 /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb INFO:: Command: (molecule-name 23) 23 /home/paule/data/greg-data/tutorial-modern.pdb 24 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 25) 25 /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: Command: (molecule-name 26) 26 /home/paule/data/greg-data/tutorial-modern.pdb 27 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 28) 28 /home/paule/data/greg-data/alt-conf-waters.pdb INFO:: Command: (molecule-name 29) 29 /home/paule/data/greg-data/backrub-fragment.pdb INFO:: Command: (molecule-name 30) 30 Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb 31 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT INFO:: Command: (molecule-name 32) 32 /home/paule/data/greg-data/test-TER-OXT.pdb INFO:: Command: (molecule-name 33) 33 /home/paule/data/greg-data/val.pdb INFO:: Command: (molecule-name 34) 34 /home/paule/data/greg-data/2yie-frag.pdb INFO:: Command: (molecule-name 35) 35 /home/paule/data/greg-data/4f8g.pdb INFO:: Command: (molecule-name 36) 36 /home/paule/data/greg-data/4f8g.pdb 37 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 38 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 39) 39 /home/paule/data/greg-data/tutorial-modern.pdb 40 Generic Masked Map 41 difference-map 44 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 45 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 46 averaged-map 47 difference-map INFO:: Command: (molecule-name 48) 48 /home/paule/data/greg-data/multi-carbo-coot-3.pdb INFO:: Command: (molecule-name 49) 49 /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb 50 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 51) 51 /home/paule/data/greg-data/monomer-VAL.pdb INFO:: Command: (molecule-name 52) 52 /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb INFO:: Command: (molecule-name 53) 53 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 54) 54 /home/paule/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 55) 55 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 56) 56 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 57) 57 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 58) 58 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 59) 59 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 60) 60 /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb INFO:: Command: (molecule-name 61) 61 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 62) 62 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 63) 63 /home/paule/data/greg-data/pdb3hfl.ent 64 /home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT INFO:: Command: (molecule-name 65) 65 Ideal-A-form-RNA INFO:: Command: (molecule-name 66) 66 Ideal-A-form-RNA INFO:: Command: (molecule-name 67) 67 Ideal-A-form-DNA INFO:: Command: (molecule-name 68) 68 Ideal-A-form-DNA INFO:: Command: (molecule-name 69) 69 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 70) 70 /home/paule/data/greg-data/some-waters-with-ter.pdb INFO:: Command: (molecule-name 71) 71 /home/paule/data/greg-data/tm+some-waters.pdb INFO:: Command: (molecule-name 72) 72 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 73) 73 /home/paule/data/greg-data/water-test-no-cell.pdb INFO:: Command: (molecule-name 74) 74 /home/paule/data/greg-data/pathological-water-test.pdb INFO:: Command: (molecule-name 75) 75 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb 76 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 77) 77 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 78) 78 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 79) 79 /home/paule/data/greg-data/pdb1hvv.ent INFO:: Command: (molecule-name 80) 80 /home/paule/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 81) 81 /home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 82) 82 SymOp_-X,-X+Y,-Z+1/3_Copy_of_79 INFO:: Command: (molecule-name 83) 83 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 84) 84 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 85) 85 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 86) 86 /home/paule/data/greg-data/pdb1py3.ent INFO:: Command: (molecule-name 87) 87 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 88) 88 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 89) 89 /home/paule/data/greg-data/2goz-manip.pdb INFO:: Command: (molecule-name 90) 90 rnase_zip_test.pdb.gz INFO:: Command: (molecule-name 91) 91 /home/paule/data/greg-data/tutorial-modern.pdb 92 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 93) 93 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 94) 94 /home/paule/data/greg-data/HOF.RES INFO:: Command: (molecule-name 95) 95 /home/paule/data/greg-data/hollander.ins 98 /home/paule/data/greg-data/insulin.fcf Diff-SigmaA INFO:: Command: (molecule-name 99) 99 atom selection from insulin.res INFO:: Command: (molecule-name 100) 100 atom selection from insulin.res INFO:: Command: (molecule-name 102) 102 /home/paule/data/greg-data/horma-p21.res INFO:: Command: (molecule-name 103) 103 new-horma.ins INFO:: Command: (molecule-name 104) 104 /home/paule/data/greg-data/crash.hat INFO:: Command: (molecule-name 105) 105 /home/paule/data/greg-data/crash.hat INFO:: Command: (molecule-name 106) 106 coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 107) 107 /home/paule/data/greg-data/monomer-3GP.pdb INFO:: Command: (molecule-name 108) 108 /home/paule/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 109) 109 /home/paule/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 110) 110 /home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 111) 111 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 112) 112 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 113) 113 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 114) 114 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 115) 115 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 116) 116 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb 117 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT 118 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT 119 Masked (by protein) INFO:: Command: (molecule-name 120) 120 Fitted ligand #0-0 INFO:: Command: (molecule-name 121) 121 Fitted ligand #1-0 INFO:: Command: (molecule-name 122) 122 Fitted ligand #2-0 INFO:: Command: (molecule-name 123) 123 Fitted ligand #3-0 INFO:: Command: (molecule-name 124) 124 Fitted ligand #4-0 INFO:: Command: (molecule-name 125) 125 Fitted ligand #5-0 INFO:: Command: (molecule-name 126) 126 Fitted ligand #6-0 INFO:: Command: (molecule-name 127) 127 Fitted ligand #7-0 INFO:: Command: (molecule-name 128) 128 Fitted ligand #8-0 INFO:: Command: (molecule-name 129) 129 Fitted ligand #9-0 INFO:: Command: (molecule-name 130) 130 coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 131) 131 Copy_of_coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 132) 132 /home/paule/data/greg-data/dipole-residues.pdb INFO:: Command: (molecule-name 133) 133 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 134) 134 /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb 135 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 136) 136 Ideal-A-form-RNA INFO:: Command: (molecule-name 137) 137 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 138) 138 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 139) 139 /home/paule/data/greg-data/1wly.pdb INFO:: Command: (molecule-name 140) 140 /home/paule/data/greg-data/1yb5.pdb INFO:: Command: (graphics-to-ca-plus-ligands-representation 140) ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2qd9.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2qd9.pdb PDB file /home/paule/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 141 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/2gtn.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/2gtn.pdb PDB file /home/paule/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 0/337 Molecule 142 read successfully DEBUG:: there were 1 types with no dictionary INFO:: reference 141 has 169 atoms selected INFO:: moving 142 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_23:45:25_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491 Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832 Translation - Angstroms 0.3207 0.6598 0.8819 INFO: core rmsd achieved: 0.2210 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1.0000 sequence identity: 100.0000% ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0230 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:: 0.0110 seconds for contour map INFO:: 0.0540 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 2 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 ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... NCS info: [['A', 'B']] ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 21 3" INFO:: read_file() chain with chain id has 121 residues Symmetry available for this molecule Molecule 148 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/insulin.res") no diffs NCS target chain has 93 peers. ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 0 biomt matrices INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 149 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_23:45:27_2018_modification_0.pdb.gz INFO:: Command: (delete-residue 149 "B" 1 "") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:45:27_2018_modification_1.pdb.gz INFO:: Command: (delete-residue 149 "B" 2 "") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:45:27_2018_modification_2.pdb.gz INFO:: Command: (delete-residue 149 "B" 3 "") INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 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 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_23:45:27_2018_modification_3.pdb.gz INFO:: Command: (seqnum-from-serial-number 149 "B" 0) INFO:: Command: (seqnum-from-serial-number 149 "B" 1) INFO:: Command: (seqnum-from-serial-number 149 "B" 2) INFO:: Command: (seqnum-from-serial-number 149 "B" 3) INFO:: Command: (seqnum-from-serial-number 149 "B" 4) INFO:: Command: (seqnum-from-serial-number 149 "B" 5) INFO:: Command: (seqnum-from-serial-number 149 "B" 6) INFO:: Command: (seqnum-from-serial-number 149 "B" 7) INFO:: Command: (seqnum-from-serial-number 149 "B" 8) INFO:: Command: (seqnum-from-serial-number 149 "B" 9) INFO:: Command: (seqnum-from-serial-number 149 "B" 10) INFO:: Command: (seqnum-from-serial-number 149 "B" 11) INFO:: Command: (seqnum-from-serial-number 149 "B" 12) INFO:: Command: (seqnum-from-serial-number 149 "B" 13) INFO:: Command: (seqnum-from-serial-number 149 "B" 14) INFO:: Command: (seqnum-from-serial-number 149 "B" 15) INFO:: Command: (seqnum-from-serial-number 149 "B" 16) INFO:: Command: (seqnum-from-serial-number 149 "B" 17) INFO:: Command: (seqnum-from-serial-number 149 "B" 18) INFO:: Command: (seqnum-from-serial-number 149 "B" 19) INFO:: Command: (seqnum-from-serial-number 149 "B" 20) INFO:: Command: (seqnum-from-serial-number 149 "B" 21) INFO:: Command: (seqnum-from-serial-number 149 "B" 22) INFO:: Command: (seqnum-from-serial-number 149 "B" 23) INFO:: Command: (seqnum-from-serial-number 149 "B" 24) INFO:: Command: (seqnum-from-serial-number 149 "B" 25) INFO:: Command: (seqnum-from-serial-number 149 "B" 26) INFO:: Command: (seqnum-from-serial-number 149 "B" 27) INFO:: Command: (seqnum-from-serial-number 149 "B" 28) INFO:: Command: (seqnum-from-serial-number 149 "B" 29) INFO:: Command: (seqnum-from-serial-number 149 "B" 30) INFO:: Command: (seqnum-from-serial-number 149 "B" 31) INFO:: Command: (seqnum-from-serial-number 149 "B" 32) INFO:: Command: (seqnum-from-serial-number 149 "B" 33) INFO:: Command: (seqnum-from-serial-number 149 "B" 34) INFO:: Command: (seqnum-from-serial-number 149 "B" 35) INFO:: Command: (seqnum-from-serial-number 149 "B" 36) INFO:: Command: (seqnum-from-serial-number 149 "B" 37) INFO:: Command: (seqnum-from-serial-number 149 "B" 38) INFO:: Command: (seqnum-from-serial-number 149 "B" 39) INFO:: Command: (seqnum-from-serial-number 149 "B" 40) INFO:: Command: (seqnum-from-serial-number 149 "B" 41) INFO:: Command: (seqnum-from-serial-number 149 "B" 42) INFO:: Command: (seqnum-from-serial-number 149 "B" 43) INFO:: Command: (seqnum-from-serial-number 149 "B" 44) INFO:: Command: (seqnum-from-serial-number 149 "B" 45) INFO:: Command: (seqnum-from-serial-number 149 "B" 46) INFO:: Command: (seqnum-from-serial-number 149 "B" 47) INFO:: Command: (seqnum-from-serial-number 149 "B" 48) INFO:: Command: (seqnum-from-serial-number 149 "B" 49) INFO:: Command: (seqnum-from-serial-number 149 "B" 50) INFO:: Command: (seqnum-from-serial-number 149 "B" 51) INFO:: Command: (seqnum-from-serial-number 149 "B" 52) INFO:: Command: (seqnum-from-serial-number 149 "B" 53) INFO:: Command: (seqnum-from-serial-number 149 "B" 54) INFO:: Command: (seqnum-from-serial-number 149 "B" 55) INFO:: Command: (seqnum-from-serial-number 149 "B" 56) INFO:: Command: (seqnum-from-serial-number 149 "B" 57) INFO:: Command: (seqnum-from-serial-number 149 "B" 58) INFO:: Command: (seqnum-from-serial-number 149 "B" 59) INFO:: Command: (seqnum-from-serial-number 149 "B" 60) INFO:: Command: (seqnum-from-serial-number 149 "B" 61) INFO:: Command: (seqnum-from-serial-number 149 "B" 62) INFO:: Command: (seqnum-from-serial-number 149 "B" 63) INFO:: Command: (seqnum-from-serial-number 149 "B" 64) INFO:: Command: (seqnum-from-serial-number 149 "B" 65) INFO:: Command: (seqnum-from-serial-number 149 "B" 66) INFO:: Command: (seqnum-from-serial-number 149 "B" 67) INFO:: Command: (seqnum-from-serial-number 149 "B" 68) INFO:: Command: (seqnum-from-serial-number 149 "B" 69) INFO:: Command: (seqnum-from-serial-number 149 "B" 70) INFO:: Command: (seqnum-from-serial-number 149 "B" 71) INFO:: Command: (seqnum-from-serial-number 149 "B" 72) INFO:: Command: (seqnum-from-serial-number 149 "B" 73) INFO:: Command: (seqnum-from-serial-number 149 "B" 74) INFO:: Command: (seqnum-from-serial-number 149 "B" 75) INFO:: Command: (seqnum-from-serial-number 149 "B" 76) INFO:: Command: (seqnum-from-serial-number 149 "B" 77) INFO:: Command: (seqnum-from-serial-number 149 "B" 78) INFO:: Command: (seqnum-from-serial-number 149 "B" 79) INFO:: Command: (seqnum-from-serial-number 149 "B" 80) INFO:: Command: (seqnum-from-serial-number 149 "B" 81) INFO:: Command: (seqnum-from-serial-number 149 "B" 82) INFO:: Command: (seqnum-from-serial-number 149 "B" 83) INFO:: Command: (seqnum-from-serial-number 149 "B" 84) INFO:: Command: (seqnum-from-serial-number 149 "B" 85) INFO:: Command: (seqnum-from-serial-number 149 "B" 86) INFO:: Command: (seqnum-from-serial-number 149 "B" 87) INFO:: Command: (seqnum-from-serial-number 149 "B" 88) INFO:: Command: (seqnum-from-serial-number 149 "B" 89) INFO:: Command: (seqnum-from-serial-number 149 "B" 90) INFO:: Command: (seqnum-from-serial-number 149 "B" 91) INFO:: Command: (seqnum-from-serial-number 149 "B" 92) INFO:: Command: (seqnum-from-serial-number 149 "B" 93) INFO:: Command: (seqnum-from-serial-number 149 "B" 94) INFO:: Command: (seqnum-from-serial-number 149 "B" 95) INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Tue_Jan__2_23:45:27_2018_modification_4.pdb.gz INFO:: Command: (mutate 149 "A" 2 "" "TRP") 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 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_23:45:27_2018_modification_5.pdb.gz ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1t6q.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1t6q.ent PDB file /home/paule/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 2 biomt matrices INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 150 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_23:45:27_2018_modification_0.pdb.gz INFO:: Command: (mutate 150 "A" 50 "" "ASP") INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" INFO:: Command: (is-solvent-chain-p 150 "B") DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 150 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 150 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_23:45:27_2018_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Tue_Jan__2_23:45:27_2018_modification_2.pdb.gz result: [True, True] ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 151 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 151 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:: Command: (copy-molecule 151) INFO:: Matching/moving molecule number 152 to 151 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_23:45:29_2018_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) chain_id A master B rtop: [[0.3394591924816796, 0.5177117455596953, 0.7853292336015637, 0.8624279581117553, 0.16197572619124062, -0.4795642617960695, -0.3754803239943135, 0.8400823844328328, -0.39150493439900846], [90.55110034747929, -91.12318261711249, -47.52179998745863]] INFO:: Matching/moving molecule number 152 to 151 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.1943 rms devi: 0.2112 max devi: 0.3583 min devi: 0.0329 INFO:: Axis orientation: ( 0.1978, -0.3281, 0.9237) INFO:: Rotation in CCP4 Polar Angles: Polar = (22.5246,-58.9204,174.877) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Tue_Jan__2_23:45:29_2018_modification_1.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.9179, -0.212, 0.3353| | -0.04702, -0.7812, -0.6226| | 0.3939, -0.5873, 0.7071| ( 57.6, -116.4, -53.95) INFO:: fractional coordinates matrix: | -0.9451, -0.1016, -0.03159| | -0.05429, -0.754, -0.9411| | 0.3009, -0.5389, 0.7071| ( -0.109, -1.522, -0.4666) chain_id C master B rtop: [[-0.9179458350933407, -0.21199297393104302, 0.33531242571467806, -0.04701514428682865, -0.7811500284294697, -0.6225706460252742, 0.39390991361284383, -0.5872508936464131, 0.7070865349227144], [57.59590387868751, -116.43599115338534, -53.953192756327674]] INFO:: Matching/moving molecule number 152 to 151 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.4174 rms devi: 0.4531 max devi: 0.7926 min devi: 0.0759 INFO:: Axis orientation: ( 0.7055, 0.6938, 0.1447) INFO:: Rotation in CCP4 Polar Angles: Polar = (98.3189,-135.478,101.097) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Tue_Jan__2_23:45:29_2018_modification_2.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.401, 0.7256, -0.5591| | 0.4417, 0.3815, 0.812| | 0.8025, -0.5726, -0.1675| ( 8.426, 15.74, -123.4) INFO:: fractional coordinates matrix: | 0.656, 0.4912, -0.1182| | 0.51, 0.1265, 1.227| | 0.6131, -0.6853, -0.1675| ( 0.1983, 0.2058, -1.067) chain_id D master B rtop: [[0.4010296958260637, 0.7256475124974693, -0.5591161513244722, 0.44169126456601965, 0.38154476969746226, 0.8119928666697639, 0.8025484470558306, -0.5725899722513011, -0.16750138448839502], [8.42628578842055, 15.739925910905619, -123.41057067974724]] INFO:: Command: (close-molecule 152) NCS ghost chain IDs pre: [['B', 'A', 'C', 'D']] NCS ghost chain IDs post: [['B', 'A', 'C', 'D']] ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... INFO:: Command: (molecule-name 0) INFO:: Command: (molecule-name 1) INFO:: Command: (molecule-name 4) INFO:: Command: (molecule-name 5) INFO:: Command: (molecule-name 6) INFO:: Command: (molecule-name 7) INFO:: Command: (molecule-name 8) INFO:: Command: (molecule-name 9) INFO:: Command: (molecule-name 10) INFO:: Command: (molecule-name 11) INFO:: Command: (molecule-name 13) INFO:: Command: (molecule-name 14) INFO:: Command: (molecule-name 15) INFO:: Command: (molecule-name 17) INFO:: Command: (molecule-name 18) INFO:: Command: (molecule-name 21) INFO:: Command: (molecule-name 22) INFO:: Command: (molecule-name 23) INFO:: Command: (molecule-name 25) INFO:: Command: (molecule-name 26) INFO:: Command: (molecule-name 28) INFO:: Command: (molecule-name 29) INFO:: Command: (molecule-name 30) INFO:: Command: (molecule-name 32) INFO:: Command: (molecule-name 33) INFO:: Command: (molecule-name 34) INFO:: Command: (molecule-name 35) INFO:: Command: (molecule-name 36) INFO:: Command: (molecule-name 39) INFO:: Command: (molecule-name 48) INFO:: Command: (molecule-name 49) INFO:: Command: (molecule-name 51) INFO:: Command: (molecule-name 52) INFO:: Command: (molecule-name 53) INFO:: Command: (molecule-name 54) INFO:: Command: (molecule-name 55) INFO:: Command: (molecule-name 56) INFO:: Command: (molecule-name 57) INFO:: Command: (molecule-name 58) INFO:: Command: (molecule-name 59) INFO:: Command: (molecule-name 60) INFO:: Command: (molecule-name 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 63) INFO:: Command: (molecule-name 65) INFO:: Command: (molecule-name 66) INFO:: Command: (molecule-name 67) INFO:: Command: (molecule-name 68) INFO:: Command: (molecule-name 69) INFO:: Command: (molecule-name 70) INFO:: Command: (molecule-name 71) INFO:: Command: (molecule-name 72) INFO:: Command: (molecule-name 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 75) INFO:: Command: (molecule-name 77) INFO:: Command: (molecule-name 78) INFO:: Command: (molecule-name 79) INFO:: Command: (molecule-name 80) INFO:: Command: (molecule-name 81) INFO:: Command: (molecule-name 82) INFO:: Command: (molecule-name 83) INFO:: Command: (molecule-name 84) INFO:: Command: (molecule-name 85) INFO:: Command: (molecule-name 86) INFO:: Command: (molecule-name 87) INFO:: Command: (molecule-name 88) INFO:: Command: (molecule-name 89) INFO:: Command: (molecule-name 90) INFO:: Command: (molecule-name 91) INFO:: Command: (molecule-name 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 95) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 100) INFO:: Command: (molecule-name 102) INFO:: Command: (molecule-name 103) INFO:: Command: (molecule-name 104) INFO:: Command: (molecule-name 105) INFO:: Command: (molecule-name 106) INFO:: Command: (molecule-name 107) INFO:: Command: (molecule-name 108) INFO:: Command: (molecule-name 109) INFO:: Command: (molecule-name 110) INFO:: Command: (molecule-name 111) INFO:: Command: (molecule-name 112) INFO:: Command: (molecule-name 113) INFO:: Command: (molecule-name 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 116) INFO:: Command: (molecule-name 120) INFO:: Command: (molecule-name 121) INFO:: Command: (molecule-name 122) INFO:: Command: (molecule-name 123) INFO:: Command: (molecule-name 124) INFO:: Command: (molecule-name 125) INFO:: Command: (molecule-name 126) INFO:: Command: (molecule-name 127) INFO:: Command: (molecule-name 128) INFO:: Command: (molecule-name 129) INFO:: Command: (molecule-name 130) INFO:: Command: (molecule-name 131) INFO:: Command: (molecule-name 132) INFO:: Command: (molecule-name 133) INFO:: Command: (molecule-name 134) INFO:: Command: (molecule-name 136) INFO:: Command: (molecule-name 137) INFO:: Command: (molecule-name 138) INFO:: Command: (molecule-name 139) INFO:: Command: (molecule-name 140) INFO:: Command: (molecule-name 141) INFO:: Command: (molecule-name 142) INFO:: Command: (close-molecule 144) INFO:: Command: (close-molecule 146) INFO:: Command: (molecule-name 148) INFO:: Command: (molecule-name 149) INFO:: Command: (molecule-name 150) INFO:: Command: (molecule-name 151) INFO:: Command: (handle-read-draw-molecule-with-recentre "/home/paule/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 153 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/home/paule/data/greg-data/1hvv_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /home/paule/data/greg-data/1hvv_sigmaa.mtz Number of OBSERVED reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.0360 seconds to read MTZ file INFO:: 0.0220 seconds to initialize map INFO:: 0.0280 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0070 seconds for contour map INFO:: 0.0960 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 154 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 154 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 154 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 154 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 154 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 154 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 154 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 154 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 154 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: Command: (molecule-name 0) INFO:: Command: (molecule-name 1) INFO:: Command: (molecule-name 4) INFO:: Command: (molecule-name 5) INFO:: Command: (molecule-name 6) INFO:: Command: (molecule-name 7) INFO:: Command: (molecule-name 8) INFO:: Command: (molecule-name 9) INFO:: Command: (molecule-name 10) INFO:: Command: (molecule-name 11) INFO:: Command: (molecule-name 13) INFO:: Command: (molecule-name 14) INFO:: Command: (molecule-name 15) INFO:: Command: (molecule-name 17) INFO:: Command: (molecule-name 18) INFO:: Command: (molecule-name 21) INFO:: Command: (molecule-name 22) INFO:: Command: (molecule-name 23) INFO:: Command: (molecule-name 25) INFO:: Command: (molecule-name 26) INFO:: Command: (molecule-name 28) INFO:: Command: (molecule-name 29) INFO:: Command: (molecule-name 30) INFO:: Command: (molecule-name 32) INFO:: Command: (molecule-name 33) INFO:: Command: (molecule-name 34) INFO:: Command: (molecule-name 35) INFO:: Command: (molecule-name 36) INFO:: Command: (molecule-name 39) INFO:: Command: (molecule-name 48) INFO:: Command: (molecule-name 49) INFO:: Command: (molecule-name 51) INFO:: Command: (molecule-name 52) INFO:: Command: (molecule-name 53) INFO:: Command: (molecule-name 54) INFO:: Command: (molecule-name 55) INFO:: Command: (molecule-name 56) INFO:: Command: (molecule-name 57) INFO:: Command: (molecule-name 58) INFO:: Command: (molecule-name 59) INFO:: Command: (molecule-name 60) INFO:: Command: (molecule-name 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 63) INFO:: Command: (molecule-name 65) INFO:: Command: (molecule-name 66) INFO:: Command: (molecule-name 67) INFO:: Command: (molecule-name 68) INFO:: Command: (molecule-name 69) INFO:: Command: (molecule-name 70) INFO:: Command: (molecule-name 71) INFO:: Command: (molecule-name 72) INFO:: Command: (molecule-name 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 75) INFO:: Command: (molecule-name 77) INFO:: Command: (molecule-name 78) INFO:: Command: (molecule-name 79) INFO:: Command: (molecule-name 80) INFO:: Command: (molecule-name 81) INFO:: Command: (molecule-name 82) INFO:: Command: (molecule-name 83) INFO:: Command: (molecule-name 84) INFO:: Command: (molecule-name 85) INFO:: Command: (molecule-name 86) INFO:: Command: (molecule-name 87) INFO:: Command: (molecule-name 88) INFO:: Command: (molecule-name 89) INFO:: Command: (molecule-name 90) INFO:: Command: (molecule-name 91) INFO:: Command: (molecule-name 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 95) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 100) INFO:: Command: (molecule-name 102) INFO:: Command: (molecule-name 103) INFO:: Command: (molecule-name 104) INFO:: Command: (molecule-name 105) INFO:: Command: (molecule-name 106) INFO:: Command: (molecule-name 107) INFO:: Command: (molecule-name 108) INFO:: Command: (molecule-name 109) INFO:: Command: (molecule-name 110) INFO:: Command: (molecule-name 111) INFO:: Command: (molecule-name 112) INFO:: Command: (molecule-name 113) INFO:: Command: (molecule-name 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 116) INFO:: Command: (molecule-name 120) INFO:: Command: (molecule-name 121) INFO:: Command: (molecule-name 122) INFO:: Command: (molecule-name 123) INFO:: Command: (molecule-name 124) INFO:: Command: (molecule-name 125) INFO:: Command: (molecule-name 126) INFO:: Command: (molecule-name 127) INFO:: Command: (molecule-name 128) INFO:: Command: (molecule-name 129) INFO:: Command: (molecule-name 130) INFO:: Command: (molecule-name 131) INFO:: Command: (molecule-name 132) INFO:: Command: (molecule-name 133) INFO:: Command: (molecule-name 134) INFO:: Command: (molecule-name 136) INFO:: Command: (molecule-name 137) INFO:: Command: (molecule-name 138) INFO:: Command: (molecule-name 139) INFO:: Command: (molecule-name 140) INFO:: Command: (molecule-name 141) INFO:: Command: (molecule-name 142) INFO:: Command: (molecule-name 148) INFO:: Command: (molecule-name 149) INFO:: Command: (molecule-name 150) INFO:: Command: (molecule-name 151) INFO:: Command: (molecule-name 153) BL DEBUG:: molecule_names ['/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/ins-code-fragment-pre.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-modern.pdb', 'mainchain', '/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb', 'regression-test-terminal-residue.pdb', 'atom selection from regression-test-terminal-residue.pdb', '/home/paule/data/greg-data/frag-2wot.pdb', 'sphere selection from tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rotamer-test-fragment.pdb', '/home/paule/data/greg-data/res098.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/pdb3knw.ent', '/home/paule/data/greg-data/pdb1py3.ent', '/home/paule/data/greg-data/alt-conf-pepflip-test.pdb', '/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/alt-conf-waters.pdb', '/home/paule/data/greg-data/backrub-fragment.pdb', 'Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT', '/home/paule/data/greg-data/test-TER-OXT.pdb', '/home/paule/data/greg-data/val.pdb', '/home/paule/data/greg-data/2yie-frag.pdb', '/home/paule/data/greg-data/4f8g.pdb', '/home/paule/data/greg-data/4f8g.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-modern.pdb', 'Generic Masked Map', 'difference-map', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'averaged-map', 'difference-map', '/home/paule/data/greg-data/multi-carbo-coot-3.pdb', '/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/monomer-VAL.pdb', '/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb', 'atom selection from tutorial-modern.pdb', '/home/paule/data/greg-data/monomer-ACT.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', 'atom selection from tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb3hfl.ent', '/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Ideal-A-form-RNA', 'Ideal-A-form-RNA', 'Ideal-A-form-DNA', 'Ideal-A-form-DNA', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/some-waters-with-ter.pdb', '/home/paule/data/greg-data/tm+some-waters.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/water-test-no-cell.pdb', '/home/paule/data/greg-data/pathological-water-test.pdb', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb1hvv.ent', '/home/paule/data/greg-data/monomer-ACT.pdb', '/home/paule/data/greg-data/monomer-NPO.pdb', 'SymOp_-X,-X+Y,-Z+1/3_Copy_of_79', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb1py3.ent', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/2goz-manip.pdb', 'rnase_zip_test.pdb.gz', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/HOF.RES', '/home/paule/data/greg-data/hollander.ins', '/home/paule/data/greg-data/insulin.fcf Diff-SigmaA', 'atom selection from insulin.res', 'atom selection from insulin.res', '/home/paule/data/greg-data/horma-p21.res', 'new-horma.ins', '/home/paule/data/greg-data/crash.hat', '/home/paule/data/greg-data/crash.hat', 'coot-ccp4/monomer-3GP.pdb', '/home/paule/data/greg-data/monomer-3GP.pdb', '/home/paule/data/greg-data/test-LIG.pdb', '/home/paule/data/greg-data/test-LIG.pdb', '/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb', '/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb', '/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT', '/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT', 'Masked (by protein)', 'Fitted ligand #0-0', 'Fitted ligand #1-0', 'Fitted ligand #2-0', 'Fitted ligand #3-0', 'Fitted ligand #4-0', 'Fitted ligand #5-0', 'Fitted ligand #6-0', 'Fitted ligand #7-0', 'Fitted ligand #8-0', 'Fitted ligand #9-0', 'coot-ccp4/monomer-3GP.pdb', 'Copy_of_coot-ccp4/monomer-3GP.pdb', '/home/paule/data/greg-data/dipole-residues.pdb', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', '/home/paule/data/greg-data/1wly.pdb', '/home/paule/data/greg-data/1yb5.pdb', '/home/paule/data/greg-data/2qd9.pdb', '/home/paule/data/greg-data/2gtn.pdb', '/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Map 2 NCS average of Chain A type molecules', 'Map 143 NCS average of Chain A type molecules', '/home/paule/data/greg-data/insulin.res', '/home/paule/data/greg-data/tutorial-modern.pdb', '/home/paule/data/greg-data/pdb1t6q.ent', '/home/paule/data/greg-data/pdb1hvv.ent', '/home/paule/data/greg-data/pdb1hvv.ent', '/home/paule/data/greg-data/1hvv_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Map 154 NCS found from matching Chain B onto Chain A', 'Map 154 NCS found from matching Chain C onto Chain A', 'Map 154 NCS found from matching Chain D onto Chain A', 'Map 154 NCS average of Chain A type molecules', 'Map 154 NCS found from matching Chain B onto Chain A', 'Map 154 NCS found from matching Chain C onto Chain A', 'Map 154 NCS found from matching Chain D onto Chain A', 'Map 154 NCS average of Chain A type molecules'] BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... INFO:: Command: (+ 2 4) INFO:: Command: (rotation-centre) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) BL DEBUG:: return scheme is [24.219083786010742, -41.04264831542969, -67.95923614501953] INFO:: Command: 2 ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... Entering test: kevin's torsion test PASS: kevin's torsion test Entering test: test_alt_conf_rotamers INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_alt_conf_rotamers Entering test: test_fragmemt_atom_selection INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 n_initial: 1465 n_1: 1401 n_2: 64 PASS: test_fragmemt_atom_selection Entering test: test_add_atom INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_add_atom Entering test: test dictionary partial charges INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NA.cif PASS: test dictionary partial charges Entering test: test segid exchange INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Test with a rogue segid INFO:: No consistent segids for residue 1 PASS: test segid exchange Entering test: test ligand from point There are 2 data in /home/paule/data/greg-data/libcheck_3GP-torsion-filtered.cif INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... non-H torsion: 0 [torsion-restraint: CONST_1 O6 C6 C5 N7 0.0000 0.0000 0 CONST ] non-H torsion: 1 [torsion-restraint: CONST_2 C6 C5 C4 N3 0.0000 0.0000 0 CONST ] non-H torsion: 2 [torsion-restraint: CONST_3 C6 C5 C4 N9 180.0000 0.0000 0 CONST ] non-H torsion: 3 [torsion-restraint: CONST_4 C5 C4 N3 C2 0.0000 0.0000 0 CONST ] non-H torsion: 4 [torsion-restraint: CONST_5 C4 N3 C2 N1 0.0000 0.0000 0 CONST ] non-H torsion: 5 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] non-H torsion: 6 [torsion-restraint: CONST_6 N3 C2 N1 C6 0.0000 0.0000 0 CONST ] non-H torsion: 7 [torsion-restraint: CONST_12 N3 C2 N1 HN1 180.0000 0.0000 0 CONST ] non-H torsion: 8 [torsion-restraint: CONST_7 C6 C5 N7 C8 180.0000 0.0000 0 CONST ] non-H torsion: 9 [torsion-restraint: CONST_8 C5 N7 C8 N9 0.0000 0.0000 0 CONST ] non-H torsion: 10 [torsion-restraint: CONST_9 N7 C8 N9 C1* 180.0000 0.0000 0 CONST ] non-H torsion: 11 [torsion-restraint: CONST_10 N7 C8 N9 C4 0.0000 0.0000 0 CONST ] non-H torsion: 12 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] non-H torsion: 13 [torsion-restraint: CONST_var_3 N9 C1* O4* C4* -152.9040 20.0000 1 CONST ] non-H torsion: 14 [torsion-restraint: CONST_var_4 C1* O4* C4* C5* 124.2120 20.0000 1 CONST ] non-H torsion: 15 [torsion-restraint: CONST_var_5 C1* O4* C4* C3* -3.5110 20.0000 1 CONST ] non-H torsion: 16 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] non-H torsion: 17 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] non-H torsion: 18 [torsion-restraint: CONST_var_8 N9 C1* C2* C3* 155.4840 20.0000 3 CONST ] non-H torsion: 19 [torsion-restraint: CONST_var_9 C1* C2* O2* HO2* 0.0000 20.0000 1 CONST ] non-H torsion: 20 [torsion-restraint: CONST_var_10 C1* C2* C3* O3* 82.0740 20.0000 3 CONST ] non-H torsion: 21 [torsion-restraint: CONST_11 C1* C2* C3* H3* -157.9260 0.0000 0 CONST ] non-H torsion: 22 [torsion-restraint: CONST_var_11 C1* C2* C3* C4* -36.8410 20.0000 3 CONST ] non-H torsion: 23 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] non-H torsion: 24 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] non-H-non-ring-non-const torsion: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] non-H-non-ring-non-const torsion: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] non-H-non-ring-non-const torsion: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] non-H-non-ring-non-const torsion: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] non-H-non-ring-non-const torsion: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] non-H-non-ring-non-const torsion: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 21.2929 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -87.1848 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] -74.5228 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] -35.2286 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -154.5149 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -140.7589 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 388 non-bonded restraints initial distortion_score: 161.5908 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.3848 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 424) at 10.9348 Final Estimated RMS Z Scores: bonds: 0.0840 angles: 0.4003 torsions: N/A planes: 0.0123 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 24.1470 93.5698 421.0620 ligand eigen vectors: | -0.07545, 0.2032, -0.9762| | -0.0788, 0.9747, 0.209| | 0.994, 0.09269, -0.05753| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 2.3552 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -89.3401 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] 25.0821 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] -14.1593 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -190.5962 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -155.3024 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 381 non-bonded restraints initial distortion_score: 29.0491 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0440 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 458) at 10.9617 Final Estimated RMS Z Scores: bonds: 0.0847 angles: 0.4006 torsions: N/A planes: 0.0129 non-bonded: 0.0003 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 23.5510 101.2770 417.1629 ligand eigen vectors: | -0.1414, 0.1854, -0.9724| | -0.2386, 0.947, 0.2153| | 0.9608, 0.2625, -0.08969| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 15.8888 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -75.0083 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] -97.6873 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] 2.8617 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -198.5997 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -143.1927 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 379 non-bonded restraints initial distortion_score: 382.1575 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.9759 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 410) at 11.4431 Final Estimated RMS Z Scores: bonds: 0.0853 angles: 0.4097 torsions: N/A planes: 0.0067 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 27.8615 90.7847 425.4283 ligand eigen vectors: | -0.121, 0.209, -0.9704| | -0.22, 0.9476, 0.2316| | 0.968, 0.2415, -0.06864| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] -29.8319 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -97.0040 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] 171.5477 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] 3.0645 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -207.7583 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -169.5433 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 380 non-bonded restraints initial distortion_score: 22.6851 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0273 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 412) at 10.8703 Final Estimated RMS Z Scores: bonds: 0.0838 angles: 0.3991 torsions: N/A planes: 0.0095 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 20.9604 97.9622 423.9726 ligand eigen vectors: | -0.1859, 0.146, -0.9717| | -0.1727, 0.9686, 0.1786| | 0.9673, 0.201, -0.1548| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] -17.8604 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -105.5864 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] -95.7140 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] -4.1793 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -188.4556 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -167.1790 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 387 non-bonded restraints initial distortion_score: 404.0375 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 1.0122 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 458) at 10.8860 Final Estimated RMS Z Scores: bonds: 0.0837 angles: 0.3995 torsions: N/A planes: 0.0105 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 21.0753 99.0045 399.9330 ligand eigen vectors: | -0.1669, 0.1487, -0.9747| | -0.03424, 0.9871, 0.1564| | 0.9854, 0.05948, -0.1596| INFO:: Protein centre at: xyz = ( 41.53, 8.726, 12.87) There are 1 clusters Here are the top 10 clusters: Number: 0 # grid points: 264 score: 146.5952 | -0.1765, 0.981, -0.08001| | 0.2847, 0.1287, 0.9499| | 0.9422, 0.1449, -0.302| ( 55.49, 9.316, 20.62) xyz = ( 3.05, 1.281, 0.8881) eigenvalues: 131.0082 2545.3515 421.9402 found distance from reference centre 0.6346 PASS: test ligand from point Entering test: test peak search non-close reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... INFO:: peak filtering: npeaks: in: 5158 out: 2105 There are 2105 peaks and 0 problem peaks PASS: test peak search non-close Entering test: test symop card 1 0 0 0 1 0 0 0 1 translations: -1.0000 0.0000 0.0000 PASS: test symop card Entering test: test rotate round vector INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 0 O6 0.9397 -> 20.0000 degrees 1 C6 0.9397 -> 20.0000 degrees 2 C5 0.9397 -> 20.0000 degrees 3 C4 0.9397 -> 20.0000 degrees 4 N3 0.9397 -> 20.0000 degrees 5 C2 0.9397 -> 20.0000 degrees 6 N2 0.9397 -> 20.0000 degrees 7 HN22 0.9397 -> 20.0000 degrees 8 HN21 0.9397 -> 20.0000 degrees 9 N1 0.9397 -> 20.0000 degrees 10 HN1 0.9397 -> 20.0000 degrees 11 N7 0.9397 -> 20.0000 degrees 12 C8 0.9397 -> 20.0000 degrees 13 H8 0.9397 -> 20.0000 degrees 16 H1* 0.9397 -> 20.0000 degrees 17 O4* 0.9397 -> 20.0000 degrees 18 C4* 0.9397 -> 20.0000 degrees 19 H4* 0.9397 -> 20.0000 degrees 20 C5* 0.9397 -> 20.0000 degrees 21 H5*1 0.9397 -> 20.0000 degrees 22 H5*2 0.9397 -> 20.0000 degrees 23 O5* 0.9397 -> 20.0000 degrees 24 HO5* 0.9397 -> 20.0000 degrees 25 C2* 0.9397 -> 20.0000 degrees 26 H2* 0.9397 -> 20.0000 degrees 27 O2* 0.9397 -> 20.0000 degrees 28 HO2* 0.9397 -> 20.0000 degrees 29 C3* 0.9397 -> 20.0000 degrees 30 H3* 0.9397 -> 20.0000 degrees 31 O3* 0.9397 -> 20.0000 degrees 32 P 0.9397 -> 20.0000 degrees 33 O1P 0.9397 -> 20.0000 degrees 34 O3P 0.9397 -> 20.0000 degrees 35 O2P 0.9397 -> 20.0000 degrees PASS: test rotate round vector Entering test: SSM sequence alignment output -- Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC -- Moving: D Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG -- Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG -- PASS: SSM sequence alignment output ok ---------------------------------------------------------------------- Ran 125 tests in 50.683s OK test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... ok test07_1 (__main__.PdbMtzTestFunctions) Auto-read bad MTZ test ... ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... ok test09_1 (__main__.PdbMtzTestFunctions) db-main makes mainchain ... ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... ok test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... ok test16_3 (__main__.PdbMtzTestFunctions) Hs are correctly swapped on a TYR ... ok test16_4 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... ok test29_1 (__main__.PdbMtzTestFunctions) Skeletonize a map ... ok test29_2 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... ok test30_1 (__main__.PdbMtzTestFunctions) Refine an NAG-ASN Link ... ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... ok test32_0 (__main__.PdbMtzTestFunctions) Test for mangling of hydrogen names from a PDB v 3.0 ... ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... ok test60_0 (__main__.PdbMtzTestFunctions) post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok test61_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... ok test62_0 (__main__.PdbMtzTestFunctions) Fix for Oliver Clarke fit by atom selection bug ... ok test999_0 (__main__.PdbMtzTestFunctions) Renumber residue range without overwriting coordinates. ... ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... ok test02_0 (__main__.LigandTestFunctions) Set Bond thickness test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... ok test05_0 (__main__.LigandTestFunctions) Move and Refine Ligand test ... ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... ok test07_0 (__main__.LigandTestFunctions) Flip residue (around eigen vectors) ... ok test08_0 (__main__.LigandTestFunctions) Test dipole ... ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... ok test10_0 (__main__.LigandTestFunctions) Pyrogen Runs OK? ... ok test11_0 (__main__.LigandTestFunctions) pyrogen dictionary does not make double-quoted atom names ... ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... ok ---------------------------------------------------------------------- Ran 125 tests in 50.683s OK Unitest skip does not exist! The following tests were skipped and marked as passed: Libcif horne Pyrogen Runs OK? pyrogen dictionary does not make double-quoted atom names INFO:: Command: (close-molecule 0) INFO:: Command: (close-molecule 1) INFO:: Command: (close-molecule 2) INFO:: Command: (close-molecule 3) INFO:: Command: (close-molecule 4) INFO:: Command: (close-molecule 5) INFO:: Command: (close-molecule 6) INFO:: Command: (close-molecule 7) INFO:: Command: (close-molecule 8) INFO:: Command: (close-molecule 9) INFO:: Command: (close-molecule 10) INFO:: Command: (close-molecule 11) INFO:: Command: (close-molecule 13) INFO:: Command: (close-molecule 14) INFO:: Command: (close-molecule 15) INFO:: Command: (close-molecule 16) INFO:: Command: (close-molecule 17) INFO:: Command: (close-molecule 18) INFO:: Command: (close-molecule 21) INFO:: Command: (close-molecule 22) INFO:: Command: (close-molecule 23) INFO:: Command: (close-molecule 24) INFO:: Command: (close-molecule 25) INFO:: Command: (close-molecule 26) INFO:: Command: (close-molecule 27) INFO:: Command: (close-molecule 28) INFO:: Command: (close-molecule 29) INFO:: Command: (close-molecule 30) INFO:: Command: (close-molecule 31) INFO:: Command: (close-molecule 32) INFO:: Command: (close-molecule 33) INFO:: Command: (close-molecule 34) INFO:: Command: (close-molecule 35) INFO:: Command: (close-molecule 36) INFO:: Command: (close-molecule 37) INFO:: Command: (close-molecule 38) INFO:: Command: (close-molecule 39) INFO:: Command: (close-molecule 40) INFO:: Command: (close-molecule 41) INFO:: Command: (close-molecule 44) INFO:: Command: (close-molecule 45) INFO:: Command: (close-molecule 46) INFO:: Command: (close-molecule 47) INFO:: Command: (close-molecule 48) INFO:: Command: (close-molecule 49) INFO:: Command: (close-molecule 50) INFO:: Command: (close-molecule 51) INFO:: Command: (close-molecule 52) INFO:: Command: (close-molecule 53) INFO:: Command: (close-molecule 54) INFO:: Command: (close-molecule 55) INFO:: Command: (close-molecule 56) INFO:: Command: (close-molecule 57) INFO:: Command: (close-molecule 58) INFO:: Command: (close-molecule 59) INFO:: Command: (close-molecule 60) INFO:: Command: (close-molecule 61) INFO:: Command: (close-molecule 62) INFO:: Command: (close-molecule 63) INFO:: Command: (close-molecule 64) INFO:: Command: (close-molecule 65) INFO:: Command: (close-molecule 66) INFO:: Command: (close-molecule 67) INFO:: Command: (close-molecule 68) INFO:: Command: (close-molecule 69) INFO:: Command: (close-molecule 70) INFO:: Command: (close-molecule 71) INFO:: Command: (close-molecule 72) INFO:: Command: (close-molecule 73) INFO:: Command: (close-molecule 74) INFO:: Command: (close-molecule 75) INFO:: Command: (close-molecule 76) INFO:: Command: (close-molecule 77) INFO:: Command: (close-molecule 78) INFO:: Command: (close-molecule 79) INFO:: Command: (close-molecule 80) INFO:: Command: (close-molecule 81) INFO:: Command: (close-molecule 82) INFO:: Command: (close-molecule 83) INFO:: Command: (close-molecule 84) INFO:: Command: (close-molecule 85) INFO:: Command: (close-molecule 86) INFO:: Command: (close-molecule 87) INFO:: Command: (close-molecule 88) INFO:: Command: (close-molecule 89) INFO:: Command: (close-molecule 90) INFO:: Command: (close-molecule 91) INFO:: Command: (close-molecule 92) INFO:: Command: (close-molecule 93) INFO:: Command: (close-molecule 94) INFO:: Command: (close-molecule 95) INFO:: Command: (close-molecule 98) INFO:: Command: (close-molecule 99) INFO:: Command: (close-molecule 100) INFO:: Command: (close-molecule 102) INFO:: Command: (close-molecule 103) INFO:: Command: (close-molecule 104) INFO:: Command: (close-molecule 105) INFO:: Command: (close-molecule 106) INFO:: Command: (close-molecule 107) INFO:: Command: (close-molecule 108) INFO:: Command: (close-molecule 109) INFO:: Command: (close-molecule 110) INFO:: Command: (close-molecule 111) INFO:: Command: (close-molecule 112) INFO:: Command: (close-molecule 113) INFO:: Command: (close-molecule 114) INFO:: Command: (close-molecule 115) INFO:: Command: (close-molecule 116) INFO:: Command: (close-molecule 117) INFO:: Command: (close-molecule 118) INFO:: Command: (close-molecule 119) INFO:: Command: (close-molecule 120) INFO:: Command: (close-molecule 121) INFO:: Command: (close-molecule 122) INFO:: Command: (close-molecule 123) INFO:: Command: (close-molecule 124) INFO:: Command: (close-molecule 125) INFO:: Command: (close-molecule 126) INFO:: Command: (close-molecule 127) INFO:: Command: (close-molecule 128) INFO:: Command: (close-molecule 129) INFO:: Command: (close-molecule 130) INFO:: Command: (close-molecule 131) INFO:: Command: (close-molecule 132) INFO:: Command: (close-molecule 133) INFO:: Command: (close-molecule 134) INFO:: Command: (close-molecule 135) INFO:: Command: (close-molecule 136) INFO:: Command: (close-molecule 137) INFO:: Command: (close-molecule 138) INFO:: Command: (close-molecule 139) INFO:: Command: (close-molecule 140) INFO:: Command: (close-molecule 141) INFO:: Command: (close-molecule 142) INFO:: Command: (close-molecule 143) INFO:: Command: (close-molecule 145) INFO:: Command: (close-molecule 147) INFO:: Command: (close-molecule 148) INFO:: Command: (close-molecule 149) INFO:: Command: (close-molecule 150) INFO:: Command: (close-molecule 151) INFO:: Command: (close-molecule 153) INFO:: Command: (close-molecule 154) INFO:: Command: (close-molecule 155) INFO:: Command: (close-molecule 156) INFO:: Command: (close-molecule 157) INFO:: Command: (close-molecule 158) INFO:: Command: (close-molecule 159) INFO:: Command: (close-molecule 160) INFO:: Command: (close-molecule 161) INFO:: Command: (close-molecule 162) gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable FINALLY collect some GARBAGE BL INFO:: no of collected carbage items 6 BL DEBUG:: list of garbage items: (, , ) Detailed information for functions: BL INFO:: garbage item and location: BL INFO:: garbage item and location: INFO:: Command: (use-graphics-interface-state) INFO:: Command: (stereo-mode-state) INFO:: Command: (stereo-mode-state) INFO:: Command: (save-state) Good evening root. Welcome to Coot 0.8.9-pre. ObjectCache: Leaked 0003 refs to ObjectCache: Leaked 0003 refs to test_coot_python: coot test passed