testing with python unittest testing with python unittest currently we are here: /home/paule/autobuild/building/ubuntu1404_2015-08-31__T14_57_15/coot-0.8.2 /home/paule/autobuild/Linux-ubuntu1404-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/ 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/a/AR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.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 INFO:: Reading coordinate file: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/standard-residues.pdb PDB file /home/paule/autobuild/Linux-ubuntu1404-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) Importing python module coot using command from coot import * INFO:: coot.py imported Running python script /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Loading: redefine_functions.py Loading: coot_utils.py Loading: filter.py Loading: coot_lsq.py Loading: shelx.py Loading: get_ebi.py Loading: local_code.py Loading: hello.py Good Afternoon None, Welcome to Coot. 0.8.2 (set-display-intro-string "Good Afternoon None, Welcome to Coot. 0.8.2") Loading: mutate.py Loading: refmac.py Loading: libcheck.py Loading: gap.py Loading: fitting.py Loading: raster3d.py Loading: povray.py Loading: remote_control.py Loading: generic_objects.py Loading: ncs.py Loading: parse_pisa_xml.py Loading: cns2coot.py Loading: clear_backup.py Loading: tips.py Loading: prodrg_import.py Loading: dictionary_generators.py Loading: jligand.py Loading: americanisms.py Loading: group_settings.py Loading: brute_lsqman.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/scheme (set-display-intro-string "Good afternoon Paul. Welcome to Coot") (set-display-lists-for-maps 0) INFO:: loading preferences file /home/paule/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 0) (unset-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 12.60) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run 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 Symmetry available for this molecule 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 No Symmetry for this model 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_Mon_Aug_31_16:13:45_2015_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_Mon_Aug_31_16:13:45_2015_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_Mon_Aug_31_16:13:45_2015_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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.035 seconds to read MTZ file INFO:: 0.01 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.018 seconds for contour map INFO:: 0.081 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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.029 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.017 seconds for contour map INFO:: 0.064 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 Symmetry available for this molecule 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-ubuntu1404-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /home/paule/autobuild/Linux-ubuntu1404-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-ubuntu1404-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /home/paule/autobuild/Linux-ubuntu1404-gtk2-python/share/coot/reference-structures/1g66.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 Symmetry available for this molecule 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 Symmetry available for this molecule 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 INFO:: Masking around 41 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 0 ALA N :: xyz = ( 49.42, 12.37, 4.385) A 0 ALA C :: xyz = ( 50.92, 13, 2.535) A 0 ALA CA :: xyz = ( 50.36, 13.37, 3.907) A 0 ALA O :: xyz = ( 52.12, 13.03, 2.265) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Aug_31_16:13:46_2015_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 Symmetry available for this molecule 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 Symmetry available for this molecule 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_Mon_Aug_31_16:13:46_2015_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 Symmetry available for this molecule 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 ... Symmetry available for this molecule 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: (setnum-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: (setnum-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: (setnum-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: (setnum-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 Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 11 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:46_2015_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 ... Symmetry available for this molecule INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (set-rotation-centre 31.46 21.41 14.82) N /10/B is not found in this molecule: (12) atom selection from tutorial-modern.pdb INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Aug_31_16:13:46_2015_modification_0.pdb.gz INFO:: Command: (delete-residue 12 "B" 10 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Aug_31_16:13:46_2015_modification_1.pdb.gz INFO:: Command: (delete-residue 12 "B" 11 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Aug_31_16:13:46_2015_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 Symmetry available for this molecule 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 Symmetry available for this molecule 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 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 9 non-bonded restraints initial distortion_score: 36.3207 Initial RMS Z values bonds: 0.404934 angles: 0.452855 torsions: N/A planes: 2.85138 non-bonded: 0 chiral vol: 0.162676 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 198) at 10.6807 Final Estimated RMS Z Scores: bonds: 0.086474 angles: 0.793863 torsions: N/A planes: 0.803328 non-bonded: 0 chiral vol: 0.69062 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 1.997 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Mon_Aug_31_16:13:47_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 Symmetry available for this molecule 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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.029 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.018 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.019 seconds for contour map INFO:: 0.068 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:47_2015_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! ------------------- (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:47_2015_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.7495 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 Symmetry available for this molecule 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 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "EDO" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3knw.ent_Mon_Aug_31_16:13:47_2015_modification_0.pdb.gz se_1: [['SE ', ''], [0.7, 2.0, 'SE', ''], [58.8, 66.533, 0.047]] se_2: [['SE ', ''], [0.7, 2.0, 'SE', ''], [60.13112002923666, 69.34847968524429, -0.673518803101735]] 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 Symmetry available for this molecule 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_Mon_Aug_31_16:13:47_2015_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 Symmetry available for this molecule 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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.028 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.017 seconds for contour map INFO:: 0.063 seconds in total INFO:: Command: (zero-occupancy-residue-range 19 "A" 37 37) here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:48_2015_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 Symmetry available for this molecule 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_Mon_Aug_31_16:13:48_2015_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 Symmetry available for this molecule 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 0x63a0770 omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Aug_31_16:13:48_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Aug_31_16:13:48_2015_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_Mon_Aug_31_16:13:48_2015_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 3 angle links 2 plane 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 0 parallel plane restraints INFO:: make_restraints(): made 31 non-bonded restraints initial distortion_score: 2187.67 Initial RMS Z values bonds: 15.4679 angles: 7.38705 torsions: N/A planes: 6.5173 non-bonded: 48.7437 chiral vol: 3.04463 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 74) at -4658.79 Final Estimated RMS Z Scores: bonds: 2.00177 angles: 1.37513 torsions: N/A planes: 3.30289 non-bonded: 1.54784 chiral vol: 0.0693062 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 2.813 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.012 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Aug_31_16:13:48_2015_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Aug_31_16:13:48_2015_modification_4.pdb.gz INFO:: Command: (mutate 22 "A" 11 "" "LEU") ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Aug_31_16:13:48_2015_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.44755 INFO:: Command: (auto-fit-best-rotamer 11 "" "" "A" 22 2 1 1.00) ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 3 angle links 2 plane 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 0 parallel plane restraints INFO:: make_restraints(): made 71 non-bonded restraints initial distortion_score: -5749.34 Initial RMS Z values bonds: 1.63748 angles: 1.69858 torsions: N/A planes: 4.82967 non-bonded: 1.36669 chiral vol: 0.521643 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 32) at -5911.56 Final Estimated RMS Z Scores: bonds: 1.79612 angles: 1.20956 torsions: N/A planes: 3.48495 non-bonded: 0.666432 chiral vol: 0.109944 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 2.883 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.011 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Aug_31_16:13:48_2015_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 Symmetry available for this molecule 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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.028 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.015 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.019 seconds for contour map INFO:: 0.064 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 0 parallel plane restraints INFO:: make_restraints(): made 6 non-bonded restraints initial distortion_score: -2708.83 Initial RMS Z values bonds: 1.67379 angles: 1.06965 torsions: N/A planes: 1.96464 non-bonded: 9.24559 chiral vol: 1.46202 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 10) at -2868.41 Final Estimated RMS Z Scores: bonds: 1.36563 angles: 1.42435 torsions: N/A planes: 2.03476 non-bonded: 4.21611 chiral vol: 0.60195 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.067 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.005 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:48_2015_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it refined moved: d= 0.301522699646 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 Symmetry available for this molecule 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 here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Aug_31_16:13:48_2015_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, '']] created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 parallel plane restraints Flanking residue restraints: 5 bond links 15 angle links 10 plane links 0 parallel plane restraints INFO:: make_restraints(): made 784 non-bonded restraints initial distortion_score: -10805.4 Initial RMS Z values bonds: 1.8061 angles: 0.891239 torsions: N/A planes: 2.12217 non-bonded: 0.000806539 chiral vol: 0.668982 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 43) at -11022.5 Final Estimated RMS Z Scores: bonds: 1.06821 angles: 0.67509 torsions: N/A planes: 1.66963 non-bonded: 0.0027605 chiral vol: 0.291895 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.287 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Aug_31_16:13:48_2015_modification_1.pdb.gz INFO:: replace_coords: 23 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it imol: 25 residues: [['A', 41, ''], ['A', 42, ''], ['A', 40, ''], ['A', 39, ''], ['A', 43, '']] created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints created 84 restraints Link restraints: 4 bond links 12 angle links 8 plane links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 1031 non-bonded restraints initial distortion_score: -12487.9 Initial RMS Z values bonds: 0.980695 angles: 1.01754 torsions: N/A planes: 9.54873 non-bonded: 0.479462 chiral vol: 10.2816 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -15840.5 Final Estimated RMS Z Scores: bonds: 1.68118 angles: 1.89155 torsions: N/A planes: 2.02423 non-bonded: 0.00587208 chiral vol: 1.84077 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.503 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Aug_31_16:13:48_2015_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ======= got bond length 1.29336675585 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 Symmetry available for this molecule 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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.028 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.015 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.02 seconds for contour map INFO:: 0.066 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 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 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -8535.71 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 10.6707 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 45) at -11574.1 Final Estimated RMS Z Scores: bonds: 1.77013 angles: 2.09282 torsions: N/A planes: 2.22538 non-bonded: 0.0187215 chiral vol: 1.98962 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.775 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.084 refinement results: ['', 0, [['Bonds', 'Bonds: 1.770', 1.770127773284912], ['Angles', 'Angles: 2.093', 2.092820644378662], ['Planes', 'Planes: 2.225', 2.2253761291503906], ['Non-bonded', 'Non-bonded: 0.137', 0.13682660460472107], ['Chirals', 'Chirals: 1.990', 1.989616870880127]]] ow factor 2.01948535442 INFO:: setting refinement weight to 14.7119362544 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 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 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -426.51 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 10.6707 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 51) at -2663.73 Final Estimated RMS Z Scores: bonds: 0.548816 angles: 1.68625 torsions: N/A planes: 1.36863 non-bonded: 0.00832746 chiral vol: 1.32222 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.945 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.171 refinement results: ['', 0, [['Bonds', 'Bonds: 0.549', 0.5488162040710449], ['Angles', 'Angles: 1.686', 1.6862517595291138], ['Planes', 'Planes: 1.369', 1.3686261177062988], ['Non-bonded', 'Non-bonded: 0.091', 0.09125491231679916], ['Chirals', 'Chirals: 1.322', 1.3222191333770752]]] ow factor 1.23147830367 INFO:: setting refinement weight to 9.70099536959 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 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 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 470.74 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 10.6707 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 67) at -1700.21 Final Estimated RMS Z Scores: bonds: 0.427833 angles: 1.63654 torsions: N/A planes: 1.16985 non-bonded: 0.00640426 chiral vol: 1.27566 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.151 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.205 refinement results: ['', 0, [['Bonds', 'Bonds: 0.428', 0.42783308029174805], ['Angles', 'Angles: 1.637', 1.6365447044372559], ['Planes', 'Planes: 1.170', 1.1698487997055054], ['Non-bonded', 'Non-bonded: 0.080', 0.08002664148807526], ['Chirals', 'Chirals: 1.276', 1.2756562232971191]]] ow factor 1.12747070193 INFO:: setting refinement weight to 7.63142727934 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 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 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 841.313 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 10.6707 non-bonded: 0.734803 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 32) at -1308.53 Final Estimated RMS Z Scores: bonds: 0.369266 angles: 1.61552 torsions: N/A planes: 1.05907 non-bonded: 0.00514072 chiral vol: 1.30419 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.77 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.619 refinement results: ['', 0, [['Bonds', 'Bonds: 0.369', 0.3692663908004761], ['Angles', 'Angles: 1.616', 1.6155202388763428], ['Planes', 'Planes: 1.059', 1.0590710639953613], ['Non-bonded', 'Non-bonded: 0.072', 0.07169884443283081], ['Chirals', 'Chirals: 1.304', 1.3041924238204956]]] ow factor 1.08701252937 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 Symmetry available for this molecule 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_Mon_Aug_31_16:13:50_2015_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 Symmetry available for this molecule 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 Symmetry available for this molecule INFO:: Command: (copy-molecule 29) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Mon_Aug_31_16:13:50_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Mon_Aug_31_16:13:50_2015_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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.029 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.017 seconds for contour map INFO:: 0.064 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 No Symmetry for this model 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_Mon_Aug_31_16:13:50_2015_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") WARNING:: This residue already has an OXT - aborting INFO:: Command: (add-OXT-to-residue 32 14 "" "A") 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 No Symmetry for this model 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_Mon_Aug_31_16:13:50_2015_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 No Symmetry for this model 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_Mon_Aug_31_16:13:50_2015_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 Symmetry available for this molecule Molecule 35 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NCO" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NCO.cif INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_Aug_31_16:13:50_2015_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 Symmetry available for this molecule Molecule 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_Aug_31_16:13:51_2015_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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.028 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.015 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.015 seconds for contour map INFO:: 0.061 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:: 0.028 seconds to read MTZ file INFO:: 0.032 seconds to initialize map INFO:: 0.032 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.033 seconds for contour map INFO:: 0.132 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 Symmetry available for this molecule 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: -0.00140323 st.d: 0.305597 Map statistics: min: -0.875045, max: 2.97757 -0.826887 9 -0.730572 46 -0.634257 403 -0.537941 2065 -0.441626 7564 -0.345311 17348 -0.248995 26177 -0.15268 33633 -0.0563644 40439 0.0399509 41126 0.136266 21610 0.232582 10119 0.328897 5756 0.425212 4384 0.521528 3595 0.617843 3168 0.714158 2681 0.810474 2161 0.906789 1759 1.0031 1314 1.09942 958 1.19574 645 1.29205 455 1.38837 271 1.48468 175 1.581 108 1.67731 59 1.77363 34 1.86994 17 1.96626 7 2.06257 2 2.15889 1 2.2552 4 2.35152 1 2.44784 0 2.54415 1 2.64047 0 2.73678 0 2.8331 0 2.92941 1 3.02573 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: [0.7261465191841125, 0.9818546772003174, 1.0008413791656494, 0.9549089670181274, 0.68085777759552, 0.7519770860671997, 0.6920666098594666, 0.5887460112571716, 0.9631485939025879, 0.9281606674194336, 0.9230127930641174] 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: -0.00140318 st.d: 0.0601239 Map statistics: min: -2.78832, max: 0.730463 -2.74433 1 -2.65636 1 -2.56839 1 -2.48042 1 -2.39245 1 -2.30448 1 -2.21651 0 -2.12854 1 -2.04057 0 -1.95261 3 -1.86464 1 -1.77667 1 -1.6887 5 -1.60073 3 -1.51276 4 -1.42479 6 -1.33682 21 -1.24885 16 -1.16088 41 -1.07291 35 -0.984941 54 -0.896972 68 -0.809003 85 -0.721033 108 -0.633064 116 -0.545094 145 -0.457125 148 -0.369155 181 -0.281186 209 -0.193216 264 -0.105247 356 -0.0172775 223669 0.0706919 639 0.158661 658 0.246631 505 0.3346 414 0.42257 223 0.510539 85 0.598509 22 0.686478 4 0.774448 0 diff-high-values: [0.008353626355528831, 0.0006559111061505973, 0.002294810488820076, 0.0019492602441459894, 0.0021293803583830595, 0.0007120085647329688, 0.0016965452814474702, -0.0023778036702424288, 0.0010665466543287039, 0.001003342098556459, 0.0025592001620680094] diff-low-values: [-0.5452420711517334, -0.9045197367668152, -0.6506662368774414, -0.7486838698387146, -0.7590927481651306, -0.9884529113769531, -1.066662073135376, -1.1893315315246582, -0.7939014434814453, -0.8879972100257874] ok test29_1 (__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 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.028 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.015 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.015 seconds for contour map INFO:: 0.061 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:: 0.028 seconds to read MTZ file INFO:: 0.046 seconds to initialize map INFO:: 0.044 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.13088e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.046 seconds for contour map INFO:: 0.173 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 108, 132, 64) by 1 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1 Map statistics: mean: -4.27711e-07 st.d: 0.311072 Map statistics: min: -0.873369, max: 2.97503 -0.825264 9 -0.729054 49 -0.632844 422 -0.536634 2147 -0.440424 7838 -0.344214 17838 -0.248005 26781 -0.151795 34418 -0.0555847 41152 0.0406252 36651 0.136835 21808 0.233045 10320 0.329255 5945 0.425465 4553 0.521675 3766 0.617885 3294 0.714095 2796 0.810305 2261 0.906514 1818 1.00272 1374 1.09893 984 1.19514 684 1.29135 472 1.38756 284 1.48377 182 1.57998 106 1.67619 63 1.7724 39 1.86861 15 1.96482 10 2.06103 2 2.15724 2 2.25345 5 2.34966 2 2.44587 1 2.54208 2 2.63829 1 2.7345 0 2.83071 1 2.92692 1 3.02313 0 Map statistics: mean: 4.28766e-07 st.d: 0.00106883 Map statistics: min: -0.00685639, max: 0.0119245 -0.00662163 5 -0.00615211 21 -0.00568258 31 -0.00521306 53 -0.00474354 114 -0.00427402 221 -0.00380449 460 -0.00333497 817 -0.00286545 1522 -0.00239593 2764 -0.0019264 4797 -0.00145688 9242 -0.00098736 19272 -0.000517837 40375 -4.83151e-05 61229 0.000421207 44298 0.00089073 20928 0.00136025 9475 0.00182977 4783 0.0022993 2778 0.00276882 1679 0.00323834 1172 0.00370786 689 0.00417739 491 0.00464691 288 0.00511643 198 0.00558595 151 0.00605548 102 0.006525 56 0.00699452 37 0.00746404 18 0.00793357 10 0.00840309 10 0.00887261 3 0.00934213 1 0.00981165 3 0.0102812 2 0.0107507 0 0.0112202 0 0.0116897 0 0.0121593 1 INFO:: map sigmas: normal 0.311072021723 and diff-map: 0.00106883328408 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-2.pdb" 1) INFO:: Reading coordinate file: /home/paule/data/greg-data/multi-carbo-coot-2.pdb PDB file /home/paule/data/greg-data/multi-carbo-coot-2.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 46 read successfully DEBUG:: there were 2 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "FUC" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/f/FUC.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAG.cif bond-length: 2.97694071154 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 parallel plane restraints INFO:: make_restraints(): made 671 non-bonded restraints initial distortion_score: 7036.75 Initial RMS Z values bonds: 11.3589 angles: 3.25886 torsions: N/A planes: 0.0835273 non-bonded: 0.0943839 chiral vol: 0.903463 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 397) at 0.747415 Final Estimated RMS Z Scores: bonds: 0.0223555 angles: 0.0902625 torsions: N/A planes: 0.00138793 non-bonded: 2.09149e-05 chiral vol: 0.046591 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.018 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-2.pdb_Mon_Aug_31_16:13:52_2015_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it bond-length: 1.44034105603 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 Symmetry available for this molecule Molecule 47 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 80) at 0.247633 Final Estimated RMS Z Scores: bonds: 0.0110165 angles: 0.0948618 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.144792 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.289 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Aug_31_16:13:52_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: undo molecule number set to: 47 INFO:: Command: (set-undo-molecule 47) INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Aug_31_16:13:52_2015_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Aug_31_16:13:52_2015_modification_0.pdb.gz PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Aug_31_16:13:52_2015_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule 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 80) at 0.247633 Final Estimated RMS Z Scores: bonds: 0.0110165 angles: 0.0948618 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.144792 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.339 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Aug_31_16:13:52_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 No Symmetry for this model Molecule 48 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: 1136.99 Initial RMS Z values bonds: 5.62114 angles: 3.43297 torsions: N/A planes: N/A non-bonded: 3.49142 chiral vol: 0.753357 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 260) at 0.473481 Final Estimated RMS Z Scores: bonds: 0.00965649 angles: 0.120847 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.138473 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.691 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Mon_Aug_31_16:13:53_2015_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... looping over restraint Symmetry available for this molecule 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: 4022.94 Initial RMS Z values bonds: 1.1515 angles: 0.847578 torsions: N/A planes: 3.05577 non-bonded: 116.199 chiral vol: 0.757848 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 46) at -476.889 Final Estimated RMS Z Scores: bonds: 0.463534 angles: 0.358931 torsions: N/A planes: 0.319157 non-bonded: 0.0242554 chiral vol: 0.0492408 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.731 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.02 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Bond-length: 2.83654797991 pass intermediate 2.8 tolerance test looping over restraint 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: 3147.02 Initial RMS Z values bonds: 17.3859 angles: 0.358931 torsions: N/A planes: 0.319157 non-bonded: 0 chiral vol: 0.0492408 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 42) at -543.484 Final Estimated RMS Z Scores: bonds: 0.129862 angles: 0.179175 torsions: N/A planes: 0.426162 non-bonded: 0 chiral vol: 0.0990418 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.757 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.018 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it OK plane atom CB Bond-length: 1.51584812793 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 Symmetry available for this molecule Molecule 50 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "ACT" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ACT.cif There are 2 data in /home/paule/data/greg-data/libcheck_ACT.cif Welcome to Coot looping over restraint 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: 5304.1 Initial RMS Z values bonds: 0.0119892 angles: 0.00653967 torsions: N/A planes: 0 non-bonded: 755.759 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 71) at -138.307 Final Estimated RMS Z Scores: bonds: 0.0323289 angles: 0.191573 torsions: N/A planes: 0.0362074 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.164 (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.045 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Mon_Aug_31_16:13:53_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it 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 Symmetry available for this molecule 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 51 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_2.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_3.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_6.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:53_2015_modification_7.pdb.gz INFO:: Command: (n-chains 51) INFO:: Command: (chain_id 51 0) INFO:: Command: (chain_id 51 1) INFO:: Command: (chain_id 51 2) INFO:: Command: (chain_id 51 3) INFO:: Command: (chain_id 51 4) INFO:: Command: (chain_id 51 5) INFO:: Command: (chain_id 51 6) INFO:: Command: (chain_id 51 7) INFO:: Command: (chain_id 51 8) ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... Symmetry available for this molecule INFO:: Command: (copy-molecule 0) Symmetry available for this molecule INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Aug_31_16:13:54_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:54_2015_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Command: (replace-fragement 52 "//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 Symmetry available for this molecule 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 54 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_Mon_Aug_31_16:13:54_2015_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 Symmetry available for this molecule 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:: Command: (turn-off-backup 55) INFO:: Command: (rotamer-score 55 "A" 28 "") Rotamer 0 : m-85 100.0 INFO:: Command: (rotamer-score 55 "A" 28 "") Rotamer 1 : t80 90.1668395996 INFO:: Command: (rotamer-score 55 "A" 28 "") Rotamer 2 : p90 50.7077865601 INFO:: Command: (rotamer-score 55 "A" 28 "") Rotamer 3 : m -30 21.4231548309 INFO:: Command: (rotamer-score 55 "A" 28 "") Rotamer 4 : m -30 21.4231548309 INFO:: Command: (turn-on-backup 55) 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 Symmetry available for this molecule INFO:: NCS chain comparison 50/87 Molecule 56 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 56 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 ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID > target seq: 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_Mon_Aug_31_16:13:55_2015_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: 696 "A" 1 ""] -> ASP [spec: 696 "A" 2 ""] -> VAL [spec: 696 "A" 3 ""] -> SER [spec: 696 "A" 11 ""] -> LEU [spec: 696 "A" 12 ""] -> PRO [spec: 696 "A" 13 ""] -> PRO [spec: 696 "A" 62 ""] -> PRO [spec: 696 "A" 63 ""] -> GLY Deletions: [spec: 696 "A" 24 ""] [spec: 696 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions INFO:: Command: (write-pdb-file 56 "mutated.pdb") ::::: [56, 'A', 1, ''] False False ::::: [56, 'A', 4, ''] True True ::::: [56, 'A', 59, ''] True True ::::: [56, 'A', 60, ''] False False ::::: [56, 'A', 61, ''] False False ::::: [56, 'A', 93, ''] True True ::::: [56, '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 Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 57 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:55_2015_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 57 "A" 10 20 100) INFO:: Command: (setnum-from-serial-number 57 "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 Symmetry available for this molecule 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 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:55_2015_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 58 "A" 10 20 -100) INFO:: Command: (setnum-from-serial-number 58 "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 No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 59 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "PCA" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PCA.cif 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:: 0.025 seconds to read MTZ file INFO:: 0.006 seconds to initialize map INFO:: 0.012 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 8.66951e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.008 seconds for contour map INFO:: 0.053 seconds in total INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_Aug_31_16:13:56_2015_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" 59 60 0 0.00) INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_Aug_31_16:13:56_2015_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 No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Aug_31_16:13:56_2015_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Aug_31_16:13:56_2015_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 61 "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 No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Aug_31_16:13:56_2015_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Aug_31_16:13:56_2015_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 62 "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 No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 63 "A" 2 "" "DC") mutated base to type DC INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 63 "A" 2 "" "DG") mutated base to type DG INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 63 "A" 2 "" "DA") mutated base to type DA INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 63 "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 No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 64 "A" 2 "" "Cd") mutated base to type Cd INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 64 "A" 2 "" "Gd") mutated base to type Gd INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 64 "A" 2 "" "Ad") mutated base to type Ad INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Aug_31_16:13:56_2015_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 64 "A" 2 "" "Td") mutated base to type Td ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... Symmetry available for this molecule 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_Mon_Aug_31_16:13:56_2015_modification_0.pdb.gz INFO:: Command: (mutate 65 "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 No Symmetry for this model Molecule 66 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_Mon_Aug_31_16:13:56_2015_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 66 "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 Symmetry available for this molecule 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 67 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 -0.0337018 stdev: 0.146071) 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 = ( 36.59, -5.925, 10.21) is too big to be water INFO:: cluster at xyz = ( 55.56, 10.24, 20.73) is too big to be water INFO:: cluster at xyz = ( 52.7, 10.79, 11.55) is too big to be water INFO:: cluster at xyz = ( 42.78, 5.832, 16.49) is too big to be water INFO:: cluster at xyz = ( 31.68, 24, 6.501) is too big to be water INFO:: cluster at xyz = ( 73.25, 12.32, 14.46) is too big to be water INFO:: cluster at xyz = ( 39.78, 8.181, 19.52) is too big to be water INFO:: cluster at xyz = ( 25.72, 4.123, 5.863) 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_Mon_Aug_31_16:13:57_2015_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Command: (write-pdb-file 67 "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 Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 68 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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_Mon_Aug_31_16:13:57_2015_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 No Symmetry for this model Molecule 69 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_water-test-no-cell.pdb_Mon_Aug_31_16:13:59_2015_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 Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 70 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_pathological-water-test.pdb_Mon_Aug_31_16:13:59_2015_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: Command: (write-pdb-file 70 "waters-moved-failure.pdb") ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... Symmetry available for this molecule 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:: 0.029 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.015 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.016 seconds for contour map INFO:: 0.063 seconds in total INFO:: Masking around 58 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 94 ALA N :: xyz = ( 58.42, 2.762, -2.12) A 94 ALA C :: xyz = ( 60.22, 2.538, -3.781) A 94 ALA CA :: xyz = ( 59.68, 2.109, -2.419) A 94 ALA O :: xyz = ( 61.35, 3.018, -3.893) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:00_2015_modification_0.pdb.gz INFO:: Command: (add-terminal-residue 71 "A" 93 1) ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... Symmetry available for this molecule INFO:: Command: (copy-molecule 0) DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 73 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 73 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_Mon_Aug_31_16:14:00_2015_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 Symmetry available for this molecule 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:: Command: (turn-off-backup 74) 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 74 "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 74 "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 74 "F" 16 20 2) INFO:: Command: (n-chains 74) INFO:: Command: (chain_id 74 0) INFO:: Command: (chain_id 74 1) INFO:: Command: (chain_id 74 2) INFO:: Command: (chain_id 74 3) INFO:: Command: (chain_id 74 4) INFO:: Command: (is-solvent-chain-p 74 "A") INFO:: Command: (is-solvent-chain-p 74 "B") INFO:: Command: (is-solvent-chain-p 74 "D") INFO:: Command: (is-solvent-chain-p 74 "E") INFO:: Command: (is-solvent-chain-p 74 "F") INFO:: Command: (renumber-residue-range 74 "E" 1 5 5) INFO:: Command: (renumber-residue-range 74 "F" 1 5 10) INFO:: Command: (turn-on-backup 74) INFO:: Command: (n-chains 74) INFO:: Command: (chain_id 74 2) INFO:: Command: (setnum-from-serial-number 74 "D" 0) INFO:: Command: (setnum-from-serial-number 74 "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 Symmetry available for this molecule 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 75 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "TAR" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TAR.cif 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 Symmetry available for this molecule Molecule 76 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 Symmetry available for this molecule Molecule 77 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NPO" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NPO.cif -------- starting chain list ----------- INFO:: Command: (n-chains 75) INFO:: Command: (chain_id 75 0) INFO:: Command: (chain_id 75 1) INFO:: Command: (chain_id 75 2) INFO:: Command: (chain_id 75 3) INFO:: Command: (chain_id 75 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 Symmetry available for this molecule INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (n-chains 75) INFO:: Command: (chain_id 75 0) INFO:: Command: (chain_id 75 1) INFO:: Command: (chain_id 75 2) INFO:: Command: (chain_id 75 3) INFO:: Command: (chain_id 75 4) INFO:: Command: (chain_id 75 5) INFO:: Command: (chain_id 75 6) INFO:: Command: (chain_id 75 7) INFO:: Command: (chain_id 75 8) INFO:: Command: (chain_id 75 9) INFO:: Command: (chain_id 75 10) INFO:: Command: (chain_id 75 11) ['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K'] INFO:: Command: (write-pdb-file 75 "sym-merged.pdb") ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... Symmetry available for this molecule INFO:: Command: (copy-molecule 0) Symmetry available for this molecule INFO:: Command: (copy-molecule 0) INFO:: Matching/moving molecule number 80 to 79 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_Mon_Aug_31_16:14:01_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal 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 Symmetry available for this molecule 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 81 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 Symmetry available for this molecule 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 82 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 81 to 82 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_Mon_Aug_31_16:14:02_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal 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 Symmetry available for this molecule 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 83 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:02_2015_modification_0.pdb.gz INFO:: Command: (set-residue-name 83 "A" 37 "" "FRE") INFO:: Command: (n-chains 83) INFO:: Command: (chain_id 83 0) INFO:: Command: (chain_id 83 1) INFO:: Command: (setnum-from-serial-number 83 "A" 0) INFO:: Command: (insertion-code-from-serial-number 83 "A" 0) INFO:: Command: (setnum-from-serial-number 83 "A" 1) INFO:: Command: (insertion-code-from-serial-number 83 "A" 1) INFO:: Command: (setnum-from-serial-number 83 "A" 2) INFO:: Command: (insertion-code-from-serial-number 83 "A" 2) INFO:: Command: (setnum-from-serial-number 83 "A" 3) INFO:: Command: (insertion-code-from-serial-number 83 "A" 3) INFO:: Command: (setnum-from-serial-number 83 "A" 4) INFO:: Command: (insertion-code-from-serial-number 83 "A" 4) INFO:: Command: (setnum-from-serial-number 83 "A" 5) INFO:: Command: (insertion-code-from-serial-number 83 "A" 5) INFO:: Command: (setnum-from-serial-number 83 "A" 6) INFO:: Command: (insertion-code-from-serial-number 83 "A" 6) INFO:: Command: (setnum-from-serial-number 83 "A" 7) INFO:: Command: (insertion-code-from-serial-number 83 "A" 7) INFO:: Command: (setnum-from-serial-number 83 "A" 8) INFO:: Command: (insertion-code-from-serial-number 83 "A" 8) INFO:: Command: (setnum-from-serial-number 83 "A" 9) INFO:: Command: (insertion-code-from-serial-number 83 "A" 9) INFO:: Command: (setnum-from-serial-number 83 "A" 10) INFO:: Command: (insertion-code-from-serial-number 83 "A" 10) INFO:: Command: (setnum-from-serial-number 83 "A" 11) INFO:: Command: (insertion-code-from-serial-number 83 "A" 11) INFO:: Command: (setnum-from-serial-number 83 "A" 12) INFO:: Command: (insertion-code-from-serial-number 83 "A" 12) INFO:: Command: (setnum-from-serial-number 83 "A" 13) INFO:: Command: (insertion-code-from-serial-number 83 "A" 13) INFO:: Command: (setnum-from-serial-number 83 "A" 14) INFO:: Command: (insertion-code-from-serial-number 83 "A" 14) INFO:: Command: (setnum-from-serial-number 83 "A" 15) INFO:: Command: (insertion-code-from-serial-number 83 "A" 15) INFO:: Command: (setnum-from-serial-number 83 "A" 16) INFO:: Command: (insertion-code-from-serial-number 83 "A" 16) INFO:: Command: (setnum-from-serial-number 83 "A" 17) INFO:: Command: (insertion-code-from-serial-number 83 "A" 17) INFO:: Command: (setnum-from-serial-number 83 "A" 18) INFO:: Command: (insertion-code-from-serial-number 83 "A" 18) INFO:: Command: (setnum-from-serial-number 83 "A" 19) INFO:: Command: (insertion-code-from-serial-number 83 "A" 19) INFO:: Command: (setnum-from-serial-number 83 "A" 20) INFO:: Command: (insertion-code-from-serial-number 83 "A" 20) INFO:: Command: (setnum-from-serial-number 83 "A" 21) INFO:: Command: (insertion-code-from-serial-number 83 "A" 21) INFO:: Command: (setnum-from-serial-number 83 "A" 22) INFO:: Command: (insertion-code-from-serial-number 83 "A" 22) INFO:: Command: (setnum-from-serial-number 83 "A" 23) INFO:: Command: (insertion-code-from-serial-number 83 "A" 23) INFO:: Command: (setnum-from-serial-number 83 "A" 24) INFO:: Command: (insertion-code-from-serial-number 83 "A" 24) INFO:: Command: (setnum-from-serial-number 83 "A" 25) INFO:: Command: (insertion-code-from-serial-number 83 "A" 25) INFO:: Command: (setnum-from-serial-number 83 "A" 26) INFO:: Command: (insertion-code-from-serial-number 83 "A" 26) INFO:: Command: (setnum-from-serial-number 83 "A" 27) INFO:: Command: (insertion-code-from-serial-number 83 "A" 27) INFO:: Command: (setnum-from-serial-number 83 "A" 28) INFO:: Command: (insertion-code-from-serial-number 83 "A" 28) INFO:: Command: (setnum-from-serial-number 83 "A" 29) INFO:: Command: (insertion-code-from-serial-number 83 "A" 29) INFO:: Command: (setnum-from-serial-number 83 "A" 30) INFO:: Command: (insertion-code-from-serial-number 83 "A" 30) INFO:: Command: (setnum-from-serial-number 83 "A" 31) INFO:: Command: (insertion-code-from-serial-number 83 "A" 31) INFO:: Command: (setnum-from-serial-number 83 "A" 32) INFO:: Command: (insertion-code-from-serial-number 83 "A" 32) INFO:: Command: (setnum-from-serial-number 83 "A" 33) INFO:: Command: (insertion-code-from-serial-number 83 "A" 33) INFO:: Command: (setnum-from-serial-number 83 "A" 34) INFO:: Command: (insertion-code-from-serial-number 83 "A" 34) INFO:: Command: (setnum-from-serial-number 83 "A" 35) INFO:: Command: (insertion-code-from-serial-number 83 "A" 35) INFO:: Command: (setnum-from-serial-number 83 "A" 36) INFO:: Command: (insertion-code-from-serial-number 83 "A" 36) INFO:: Command: (setnum-from-serial-number 83 "A" 37) INFO:: Command: (insertion-code-from-serial-number 83 "A" 37) INFO:: Command: (setnum-from-serial-number 83 "A" 38) INFO:: Command: (insertion-code-from-serial-number 83 "A" 38) INFO:: Command: (setnum-from-serial-number 83 "A" 39) INFO:: Command: (insertion-code-from-serial-number 83 "A" 39) INFO:: Command: (setnum-from-serial-number 83 "A" 40) INFO:: Command: (insertion-code-from-serial-number 83 "A" 40) INFO:: Command: (setnum-from-serial-number 83 "A" 41) INFO:: Command: (insertion-code-from-serial-number 83 "A" 41) INFO:: Command: (setnum-from-serial-number 83 "A" 42) INFO:: Command: (insertion-code-from-serial-number 83 "A" 42) INFO:: Command: (setnum-from-serial-number 83 "A" 43) INFO:: Command: (insertion-code-from-serial-number 83 "A" 43) INFO:: Command: (setnum-from-serial-number 83 "A" 44) INFO:: Command: (insertion-code-from-serial-number 83 "A" 44) INFO:: Command: (setnum-from-serial-number 83 "A" 45) INFO:: Command: (insertion-code-from-serial-number 83 "A" 45) INFO:: Command: 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(insertion-code-from-serial-number 83 "B" 95) 0 [83, 'A', 1, ''] 1 [83, 'A', 2, ''] 2 [83, 'A', 3, ''] 3 [83, 'A', 4, ''] 4 [83, 'A', 5, ''] 5 [83, 'A', 6, ''] 6 [83, 'A', 7, ''] 7 [83, 'A', 8, ''] 8 [83, 'A', 9, ''] 9 [83, 'A', 10, ''] 10 [83, 'A', 11, ''] 11 [83, 'A', 12, ''] 12 [83, 'A', 13, ''] 13 [83, 'A', 14, ''] 14 [83, 'A', 15, ''] 15 [83, 'A', 16, ''] 16 [83, 'A', 17, ''] 17 [83, 'A', 18, ''] 18 [83, 'A', 19, ''] 19 [83, 'A', 20, ''] 20 [83, 'A', 21, ''] 21 [83, 'A', 22, ''] 22 [83, 'A', 23, ''] 23 [83, 'A', 24, ''] 24 [83, 'A', 25, ''] 25 [83, 'A', 26, ''] 26 [83, 'A', 27, ''] 27 [83, 'A', 28, ''] 28 [83, 'A', 29, ''] 29 [83, 'A', 30, ''] 30 [83, 'A', 31, ''] 31 [83, 'A', 32, ''] 32 [83, 'A', 33, ''] 33 [83, 'A', 34, ''] 34 [83, 'A', 35, ''] 35 [83, 'A', 36, ''] 36 [83, 'A', 37, ''] 36 [83, 'A', 37, ''] 37 [83, 'A', 38, ''] 38 [83, 'A', 39, ''] 39 [83, 'A', 40, ''] 40 [83, 'A', 41, ''] 41 [83, 'A', 42, ''] 42 [83, 'A', 43, ''] 43 [83, 'A', 44, ''] 44 [83, 'A', 45, ''] 45 [83, 'A', 46, ''] 46 [83, 'A', 47, ''] 47 [83, 'A', 48, ''] 48 [83, 'A', 49, ''] 49 [83, 'A', 50, ''] 50 [83, 'A', 51, ''] 51 [83, 'A', 52, ''] 52 [83, 'A', 53, ''] 53 [83, 'A', 54, ''] 54 [83, 'A', 55, ''] 55 [83, 'A', 56, ''] 56 [83, 'A', 57, ''] 57 [83, 'A', 58, ''] 58 [83, 'A', 59, ''] 59 [83, 'A', 60, ''] 60 [83, 'A', 61, ''] 61 [83, 'A', 62, ''] 62 [83, 'A', 63, ''] 63 [83, 'A', 64, ''] 64 [83, 'A', 65, ''] 65 [83, 'A', 66, ''] 66 [83, 'A', 67, ''] 67 [83, 'A', 68, ''] 68 [83, 'A', 69, ''] 69 [83, 'A', 70, ''] 70 [83, 'A', 71, ''] 71 [83, 'A', 72, ''] 72 [83, 'A', 73, ''] 73 [83, 'A', 74, ''] 74 [83, 'A', 75, ''] 75 [83, 'A', 76, ''] 76 [83, 'A', 77, ''] 77 [83, 'A', 78, ''] 78 [83, 'A', 79, ''] 79 [83, 'A', 80, ''] 80 [83, 'A', 81, ''] 81 [83, 'A', 82, ''] 82 [83, 'A', 83, ''] 83 [83, 'A', 84, ''] 84 [83, 'A', 85, ''] 85 [83, 'A', 86, ''] 86 [83, 'A', 87, ''] 87 [83, 'A', 88, ''] 88 [83, 'A', 89, ''] 89 [83, 'A', 90, ''] 90 [83, 'A', 91, ''] 91 [83, 'A', 92, ''] 92 [83, 'A', 93, ''] 93 [83, 'B', 1, ''] 94 [83, 'B', 2, ''] 95 [83, 'B', 3, ''] 96 [83, 'B', 4, ''] 97 [83, 'B', 5, ''] 98 [83, 'B', 6, ''] 99 [83, 'B', 7, ''] 100 [83, 'B', 8, ''] 101 [83, 'B', 9, ''] 102 [83, 'B', 10, ''] 103 [83, 'B', 11, ''] 104 [83, 'B', 12, ''] 105 [83, 'B', 13, ''] 106 [83, 'B', 14, ''] 107 [83, 'B', 15, ''] 108 [83, 'B', 16, ''] 109 [83, 'B', 17, ''] 110 [83, 'B', 18, ''] 111 [83, 'B', 19, ''] 112 [83, 'B', 20, ''] 113 [83, 'B', 21, ''] 114 [83, 'B', 22, ''] 115 [83, 'B', 23, ''] 116 [83, 'B', 24, ''] 117 [83, 'B', 25, ''] 118 [83, 'B', 26, ''] 119 [83, 'B', 27, ''] 120 [83, 'B', 28, ''] 121 [83, 'B', 29, ''] 122 [83, 'B', 30, ''] 123 [83, 'B', 31, ''] 124 [83, 'B', 32, ''] 125 [83, 'B', 33, ''] 126 [83, 'B', 34, ''] 127 [83, 'B', 35, ''] 128 [83, 'B', 36, ''] 129 [83, 'B', 37, ''] 130 [83, 'B', 38, ''] 131 [83, 'B', 39, ''] 132 [83, 'B', 40, ''] 133 [83, 'B', 41, ''] 134 [83, 'B', 42, ''] 135 [83, 'B', 43, ''] 136 [83, 'B', 44, ''] 137 [83, 'B', 45, ''] 138 [83, 'B', 46, ''] 139 [83, 'B', 47, ''] 140 [83, 'B', 48, ''] 141 [83, 'B', 49, ''] 142 [83, 'B', 50, ''] 143 [83, 'B', 51, ''] 144 [83, 'B', 52, ''] 145 [83, 'B', 53, ''] 146 [83, 'B', 54, ''] 147 [83, 'B', 55, ''] 148 [83, 'B', 56, ''] 149 [83, 'B', 57, ''] 150 [83, 'B', 58, ''] 151 [83, 'B', 59, ''] 152 [83, 'B', 60, ''] 153 [83, 'B', 61, ''] 154 [83, 'B', 62, ''] 155 [83, 'B', 63, ''] 156 [83, 'B', 64, ''] 157 [83, 'B', 65, ''] 158 [83, 'B', 66, ''] 159 [83, 'B', 67, ''] 160 [83, 'B', 68, ''] 161 [83, 'B', 69, ''] 162 [83, 'B', 70, ''] 163 [83, 'B', 71, ''] 164 [83, 'B', 72, ''] 165 [83, 'B', 73, ''] 166 [83, 'B', 74, ''] 167 [83, 'B', 75, ''] 168 [83, 'B', 76, ''] 169 [83, 'B', 77, ''] 170 [83, 'B', 78, ''] 171 [83, 'B', 79, ''] 172 [83, 'B', 80, ''] 173 [83, 'B', 81, ''] 174 [83, 'B', 82, ''] 175 [83, 'B', 83, ''] 176 [83, 'B', 84, ''] 177 [83, 'B', 85, ''] 178 [83, 'B', 86, ''] 179 [83, 'B', 87, ''] 180 [83, 'B', 88, ''] 181 [83, 'B', 89, ''] 182 [83, 'B', 90, ''] 183 [83, 'B', 91, ''] 184 [83, 'B', 92, ''] 185 [83, 'B', 93, ''] 186 [83, 'B', 94, ''] 187 [83, 'B', 95, ''] 188 [83, '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 Symmetry available for this molecule 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 84 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (n-chains 84) INFO:: Command: (chain_id 84 0) INFO:: Command: (chain_id 84 1) INFO:: Command: (setnum-from-serial-number 84 "A" 0) INFO:: Command: (insertion-code-from-serial-number 84 "A" 0) INFO:: Command: (setnum-from-serial-number 84 "A" 1) INFO:: Command: (insertion-code-from-serial-number 84 "A" 1) INFO:: Command: (setnum-from-serial-number 84 "A" 2) INFO:: Command: (insertion-code-from-serial-number 84 "A" 2) INFO:: Command: (setnum-from-serial-number 84 "A" 3) INFO:: Command: (insertion-code-from-serial-number 84 "A" 3) INFO:: Command: (setnum-from-serial-number 84 "A" 4) INFO:: Command: (insertion-code-from-serial-number 84 "A" 4) INFO:: Command: (setnum-from-serial-number 84 "A" 5) INFO:: Command: (insertion-code-from-serial-number 84 "A" 5) INFO:: Command: (setnum-from-serial-number 84 "A" 6) INFO:: Command: (insertion-code-from-serial-number 84 "A" 6) INFO:: Command: (setnum-from-serial-number 84 "A" 7) INFO:: Command: (insertion-code-from-serial-number 84 "A" 7) INFO:: Command: (setnum-from-serial-number 84 "A" 8) INFO:: Command: (insertion-code-from-serial-number 84 "A" 8) INFO:: Command: (setnum-from-serial-number 84 "A" 9) INFO:: Command: (insertion-code-from-serial-number 84 "A" 9) INFO:: Command: (setnum-from-serial-number 84 "A" 10) INFO:: Command: (insertion-code-from-serial-number 84 "A" 10) INFO:: Command: (setnum-from-serial-number 84 "A" 11) INFO:: Command: (insertion-code-from-serial-number 84 "A" 11) INFO:: Command: (setnum-from-serial-number 84 "A" 12) INFO:: Command: (insertion-code-from-serial-number 84 "A" 12) INFO:: Command: (setnum-from-serial-number 84 "A" 13) INFO:: Command: (insertion-code-from-serial-number 84 "A" 13) INFO:: Command: (setnum-from-serial-number 84 "A" 14) INFO:: Command: (insertion-code-from-serial-number 84 "A" 14) INFO:: Command: (setnum-from-serial-number 84 "A" 15) INFO:: Command: (insertion-code-from-serial-number 84 "A" 15) INFO:: Command: (setnum-from-serial-number 84 "A" 16) INFO:: Command: (insertion-code-from-serial-number 84 "A" 16) INFO:: Command: (setnum-from-serial-number 84 "A" 17) INFO:: Command: (insertion-code-from-serial-number 84 "A" 17) INFO:: Command: (setnum-from-serial-number 84 "A" 18) INFO:: Command: (insertion-code-from-serial-number 84 "A" 18) INFO:: Command: (setnum-from-serial-number 84 "A" 19) INFO:: Command: (insertion-code-from-serial-number 84 "A" 19) INFO:: Command: (setnum-from-serial-number 84 "A" 20) INFO:: Command: (insertion-code-from-serial-number 84 "A" 20) INFO:: Command: (setnum-from-serial-number 84 "A" 21) INFO:: Command: (insertion-code-from-serial-number 84 "A" 21) INFO:: Command: (setnum-from-serial-number 84 "A" 22) INFO:: Command: (insertion-code-from-serial-number 84 "A" 22) INFO:: Command: (setnum-from-serial-number 84 "A" 23) INFO:: Command: (insertion-code-from-serial-number 84 "A" 23) INFO:: Command: (setnum-from-serial-number 84 "A" 24) INFO:: Command: (insertion-code-from-serial-number 84 "A" 24) INFO:: Command: (setnum-from-serial-number 84 "A" 25) INFO:: Command: (insertion-code-from-serial-number 84 "A" 25) INFO:: Command: (setnum-from-serial-number 84 "A" 26) INFO:: Command: (insertion-code-from-serial-number 84 "A" 26) INFO:: Command: (setnum-from-serial-number 84 "A" 27) INFO:: Command: (insertion-code-from-serial-number 84 "A" 27) INFO:: Command: (setnum-from-serial-number 84 "A" 28) INFO:: Command: (insertion-code-from-serial-number 84 "A" 28) INFO:: Command: (setnum-from-serial-number 84 "A" 29) INFO:: Command: (insertion-code-from-serial-number 84 "A" 29) INFO:: Command: (setnum-from-serial-number 84 "A" 30) INFO:: Command: (insertion-code-from-serial-number 84 "A" 30) INFO:: Command: (setnum-from-serial-number 84 "A" 31) INFO:: Command: (insertion-code-from-serial-number 84 "A" 31) INFO:: Command: (setnum-from-serial-number 84 "A" 32) INFO:: Command: (insertion-code-from-serial-number 84 "A" 32) INFO:: Command: (setnum-from-serial-number 84 "A" 33) INFO:: Command: (insertion-code-from-serial-number 84 "A" 33) INFO:: Command: (setnum-from-serial-number 84 "A" 34) INFO:: Command: (insertion-code-from-serial-number 84 "A" 34) INFO:: Command: (setnum-from-serial-number 84 "A" 35) INFO:: Command: (insertion-code-from-serial-number 84 "A" 35) INFO:: Command: (setnum-from-serial-number 84 "A" 36) INFO:: Command: (insertion-code-from-serial-number 84 "A" 36) INFO:: Command: (setnum-from-serial-number 84 "A" 37) INFO:: Command: (insertion-code-from-serial-number 84 "A" 37) INFO:: Command: (setnum-from-serial-number 84 "A" 38) INFO:: Command: (insertion-code-from-serial-number 84 "A" 38) INFO:: Command: (setnum-from-serial-number 84 "A" 39) INFO:: Command: (insertion-code-from-serial-number 84 "A" 39) INFO:: Command: (setnum-from-serial-number 84 "A" 40) INFO:: Command: (insertion-code-from-serial-number 84 "A" 40) INFO:: Command: (setnum-from-serial-number 84 "A" 41) INFO:: Command: (insertion-code-from-serial-number 84 "A" 41) INFO:: Command: (setnum-from-serial-number 84 "A" 42) INFO:: Command: (insertion-code-from-serial-number 84 "A" 42) INFO:: Command: (setnum-from-serial-number 84 "A" 43) INFO:: Command: (insertion-code-from-serial-number 84 "A" 43) INFO:: Command: (setnum-from-serial-number 84 "A" 44) INFO:: Command: (insertion-code-from-serial-number 84 "A" 44) INFO:: Command: (setnum-from-serial-number 84 "A" 45) INFO:: Command: (insertion-code-from-serial-number 84 "A" 45) INFO:: Command: (setnum-from-serial-number 84 "A" 46) INFO:: Command: (insertion-code-from-serial-number 84 "A" 46) INFO:: Command: (setnum-from-serial-number 84 "A" 47) INFO:: Command: (insertion-code-from-serial-number 84 "A" 47) INFO:: Command: (setnum-from-serial-number 84 "A" 48) INFO:: Command: (insertion-code-from-serial-number 84 "A" 48) INFO:: Command: (setnum-from-serial-number 84 "A" 49) INFO:: Command: (insertion-code-from-serial-number 84 "A" 49) INFO:: Command: (setnum-from-serial-number 84 "A" 50) INFO:: Command: (insertion-code-from-serial-number 84 "A" 50) INFO:: Command: (setnum-from-serial-number 84 "A" 51) INFO:: Command: (insertion-code-from-serial-number 84 "A" 51) INFO:: Command: (setnum-from-serial-number 84 "A" 52) INFO:: Command: (insertion-code-from-serial-number 84 "A" 52) INFO:: Command: (setnum-from-serial-number 84 "A" 53) INFO:: Command: (insertion-code-from-serial-number 84 "A" 53) INFO:: Command: (setnum-from-serial-number 84 "A" 54) INFO:: Command: (insertion-code-from-serial-number 84 "A" 54) INFO:: Command: (setnum-from-serial-number 84 "A" 55) INFO:: Command: (insertion-code-from-serial-number 84 "A" 55) INFO:: Command: (setnum-from-serial-number 84 "A" 56) INFO:: Command: (insertion-code-from-serial-number 84 "A" 56) INFO:: Command: (setnum-from-serial-number 84 "A" 57) INFO:: Command: (insertion-code-from-serial-number 84 "A" 57) INFO:: Command: (setnum-from-serial-number 84 "A" 58) INFO:: Command: (insertion-code-from-serial-number 84 "A" 58) INFO:: Command: (setnum-from-serial-number 84 "A" 59) INFO:: Command: (insertion-code-from-serial-number 84 "A" 59) INFO:: Command: (setnum-from-serial-number 84 "A" 60) INFO:: Command: (insertion-code-from-serial-number 84 "A" 60) INFO:: Command: (setnum-from-serial-number 84 "A" 61) INFO:: Command: (insertion-code-from-serial-number 84 "A" 61) INFO:: Command: (setnum-from-serial-number 84 "A" 62) INFO:: Command: (insertion-code-from-serial-number 84 "A" 62) INFO:: Command: (setnum-from-serial-number 84 "A" 63) INFO:: Command: (insertion-code-from-serial-number 84 "A" 63) INFO:: Command: (setnum-from-serial-number 84 "A" 64) INFO:: Command: (insertion-code-from-serial-number 84 "A" 64) INFO:: Command: (setnum-from-serial-number 84 "A" 65) INFO:: Command: (insertion-code-from-serial-number 84 "A" 65) INFO:: Command: (setnum-from-serial-number 84 "A" 66) INFO:: Command: (insertion-code-from-serial-number 84 "A" 66) INFO:: Command: (setnum-from-serial-number 84 "A" 67) INFO:: Command: (insertion-code-from-serial-number 84 "A" 67) INFO:: Command: (setnum-from-serial-number 84 "A" 68) INFO:: Command: (insertion-code-from-serial-number 84 "A" 68) INFO:: Command: (setnum-from-serial-number 84 "A" 69) INFO:: Command: (insertion-code-from-serial-number 84 "A" 69) INFO:: Command: (setnum-from-serial-number 84 "A" 70) INFO:: Command: (insertion-code-from-serial-number 84 "A" 70) INFO:: Command: (setnum-from-serial-number 84 "A" 71) INFO:: Command: (insertion-code-from-serial-number 84 "A" 71) INFO:: Command: (setnum-from-serial-number 84 "A" 72) INFO:: Command: (insertion-code-from-serial-number 84 "A" 72) INFO:: Command: (setnum-from-serial-number 84 "A" 73) INFO:: Command: (insertion-code-from-serial-number 84 "A" 73) INFO:: Command: (setnum-from-serial-number 84 "A" 74) INFO:: Command: (insertion-code-from-serial-number 84 "A" 74) INFO:: Command: (setnum-from-serial-number 84 "A" 75) INFO:: Command: (insertion-code-from-serial-number 84 "A" 75) INFO:: Command: (setnum-from-serial-number 84 "A" 76) INFO:: Command: (insertion-code-from-serial-number 84 "A" 76) INFO:: Command: (setnum-from-serial-number 84 "A" 77) INFO:: Command: (insertion-code-from-serial-number 84 "A" 77) INFO:: Command: (setnum-from-serial-number 84 "A" 78) INFO:: Command: (insertion-code-from-serial-number 84 "A" 78) INFO:: Command: (setnum-from-serial-number 84 "A" 79) INFO:: Command: (insertion-code-from-serial-number 84 "A" 79) INFO:: Command: (setnum-from-serial-number 84 "A" 80) INFO:: Command: (insertion-code-from-serial-number 84 "A" 80) INFO:: Command: (setnum-from-serial-number 84 "A" 81) INFO:: Command: (insertion-code-from-serial-number 84 "A" 81) INFO:: Command: (setnum-from-serial-number 84 "A" 82) INFO:: Command: (insertion-code-from-serial-number 84 "A" 82) INFO:: Command: (setnum-from-serial-number 84 "A" 83) INFO:: Command: (insertion-code-from-serial-number 84 "A" 83) INFO:: Command: (setnum-from-serial-number 84 "A" 84) INFO:: Command: (insertion-code-from-serial-number 84 "A" 84) INFO:: Command: (setnum-from-serial-number 84 "A" 85) INFO:: Command: (insertion-code-from-serial-number 84 "A" 85) INFO:: Command: (setnum-from-serial-number 84 "A" 86) INFO:: Command: (insertion-code-from-serial-number 84 "A" 86) INFO:: Command: (setnum-from-serial-number 84 "A" 87) INFO:: Command: (insertion-code-from-serial-number 84 "A" 87) INFO:: Command: (setnum-from-serial-number 84 "A" 88) INFO:: Command: (insertion-code-from-serial-number 84 "A" 88) INFO:: Command: (setnum-from-serial-number 84 "A" 89) INFO:: Command: (insertion-code-from-serial-number 84 "A" 89) INFO:: Command: (setnum-from-serial-number 84 "A" 90) INFO:: Command: (insertion-code-from-serial-number 84 "A" 90) INFO:: Command: (setnum-from-serial-number 84 "A" 91) INFO:: Command: (insertion-code-from-serial-number 84 "A" 91) INFO:: Command: (setnum-from-serial-number 84 "A" 92) INFO:: Command: (insertion-code-from-serial-number 84 "A" 92) INFO:: Command: (setnum-from-serial-number 84 "B" 0) INFO:: Command: (insertion-code-from-serial-number 84 "B" 0) INFO:: Command: (setnum-from-serial-number 84 "B" 1) INFO:: Command: (insertion-code-from-serial-number 84 "B" 1) INFO:: Command: (setnum-from-serial-number 84 "B" 2) INFO:: Command: (insertion-code-from-serial-number 84 "B" 2) INFO:: Command: (setnum-from-serial-number 84 "B" 3) INFO:: Command: (insertion-code-from-serial-number 84 "B" 3) INFO:: Command: (setnum-from-serial-number 84 "B" 4) INFO:: Command: (insertion-code-from-serial-number 84 "B" 4) INFO:: Command: (setnum-from-serial-number 84 "B" 5) INFO:: Command: (insertion-code-from-serial-number 84 "B" 5) INFO:: Command: (setnum-from-serial-number 84 "B" 6) INFO:: Command: (insertion-code-from-serial-number 84 "B" 6) INFO:: Command: (setnum-from-serial-number 84 "B" 7) INFO:: Command: (insertion-code-from-serial-number 84 "B" 7) INFO:: Command: (setnum-from-serial-number 84 "B" 8) INFO:: Command: (insertion-code-from-serial-number 84 "B" 8) INFO:: Command: (setnum-from-serial-number 84 "B" 9) INFO:: Command: (insertion-code-from-serial-number 84 "B" 9) INFO:: Command: (setnum-from-serial-number 84 "B" 10) INFO:: Command: (insertion-code-from-serial-number 84 "B" 10) INFO:: Command: (setnum-from-serial-number 84 "B" 11) INFO:: Command: (insertion-code-from-serial-number 84 "B" 11) INFO:: Command: (setnum-from-serial-number 84 "B" 12) INFO:: Command: (insertion-code-from-serial-number 84 "B" 12) INFO:: Command: (setnum-from-serial-number 84 "B" 13) INFO:: Command: (insertion-code-from-serial-number 84 "B" 13) INFO:: Command: (setnum-from-serial-number 84 "B" 14) INFO:: Command: (insertion-code-from-serial-number 84 "B" 14) INFO:: Command: (setnum-from-serial-number 84 "B" 15) INFO:: Command: (insertion-code-from-serial-number 84 "B" 15) INFO:: Command: (setnum-from-serial-number 84 "B" 16) INFO:: Command: (insertion-code-from-serial-number 84 "B" 16) INFO:: Command: (setnum-from-serial-number 84 "B" 17) INFO:: Command: (insertion-code-from-serial-number 84 "B" 17) INFO:: Command: (setnum-from-serial-number 84 "B" 18) INFO:: Command: (insertion-code-from-serial-number 84 "B" 18) INFO:: Command: (setnum-from-serial-number 84 "B" 19) INFO:: Command: (insertion-code-from-serial-number 84 "B" 19) INFO:: Command: (setnum-from-serial-number 84 "B" 20) INFO:: Command: (insertion-code-from-serial-number 84 "B" 20) INFO:: Command: (setnum-from-serial-number 84 "B" 21) INFO:: Command: (insertion-code-from-serial-number 84 "B" 21) INFO:: Command: (setnum-from-serial-number 84 "B" 22) INFO:: Command: (insertion-code-from-serial-number 84 "B" 22) INFO:: Command: (setnum-from-serial-number 84 "B" 23) INFO:: Command: (insertion-code-from-serial-number 84 "B" 23) INFO:: Command: (setnum-from-serial-number 84 "B" 24) INFO:: Command: (insertion-code-from-serial-number 84 "B" 24) INFO:: Command: (setnum-from-serial-number 84 "B" 25) INFO:: Command: (insertion-code-from-serial-number 84 "B" 25) INFO:: Command: (setnum-from-serial-number 84 "B" 26) INFO:: Command: (insertion-code-from-serial-number 84 "B" 26) INFO:: Command: (setnum-from-serial-number 84 "B" 27) INFO:: Command: (insertion-code-from-serial-number 84 "B" 27) INFO:: Command: (setnum-from-serial-number 84 "B" 28) INFO:: Command: (insertion-code-from-serial-number 84 "B" 28) INFO:: Command: (setnum-from-serial-number 84 "B" 29) INFO:: Command: (insertion-code-from-serial-number 84 "B" 29) INFO:: Command: (setnum-from-serial-number 84 "B" 30) INFO:: Command: (insertion-code-from-serial-number 84 "B" 30) INFO:: Command: (setnum-from-serial-number 84 "B" 31) INFO:: Command: (insertion-code-from-serial-number 84 "B" 31) INFO:: Command: (setnum-from-serial-number 84 "B" 32) INFO:: Command: (insertion-code-from-serial-number 84 "B" 32) INFO:: Command: (setnum-from-serial-number 84 "B" 33) INFO:: Command: (insertion-code-from-serial-number 84 "B" 33) INFO:: Command: (setnum-from-serial-number 84 "B" 34) INFO:: Command: (insertion-code-from-serial-number 84 "B" 34) INFO:: Command: (setnum-from-serial-number 84 "B" 35) INFO:: Command: (insertion-code-from-serial-number 84 "B" 35) INFO:: Command: (setnum-from-serial-number 84 "B" 36) INFO:: Command: (insertion-code-from-serial-number 84 "B" 36) INFO:: Command: (setnum-from-serial-number 84 "B" 37) INFO:: Command: (insertion-code-from-serial-number 84 "B" 37) INFO:: Command: (setnum-from-serial-number 84 "B" 38) INFO:: Command: (insertion-code-from-serial-number 84 "B" 38) INFO:: Command: (setnum-from-serial-number 84 "B" 39) INFO:: Command: (insertion-code-from-serial-number 84 "B" 39) INFO:: Command: (setnum-from-serial-number 84 "B" 40) INFO:: Command: (insertion-code-from-serial-number 84 "B" 40) INFO:: Command: (setnum-from-serial-number 84 "B" 41) INFO:: Command: (insertion-code-from-serial-number 84 "B" 41) INFO:: Command: (setnum-from-serial-number 84 "B" 42) INFO:: Command: (insertion-code-from-serial-number 84 "B" 42) INFO:: Command: (setnum-from-serial-number 84 "B" 43) INFO:: Command: (insertion-code-from-serial-number 84 "B" 43) INFO:: Command: (setnum-from-serial-number 84 "B" 44) INFO:: Command: (insertion-code-from-serial-number 84 "B" 44) INFO:: Command: (setnum-from-serial-number 84 "B" 45) INFO:: Command: (insertion-code-from-serial-number 84 "B" 45) INFO:: Command: (setnum-from-serial-number 84 "B" 46) INFO:: Command: (insertion-code-from-serial-number 84 "B" 46) INFO:: Command: (setnum-from-serial-number 84 "B" 47) INFO:: Command: (insertion-code-from-serial-number 84 "B" 47) INFO:: Command: 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(insertion-code-from-serial-number 84 "B" 90) INFO:: Command: (setnum-from-serial-number 84 "B" 91) INFO:: Command: (insertion-code-from-serial-number 84 "B" 91) INFO:: Command: (setnum-from-serial-number 84 "B" 92) INFO:: Command: (insertion-code-from-serial-number 84 "B" 92) INFO:: Command: (setnum-from-serial-number 84 "B" 93) INFO:: Command: (insertion-code-from-serial-number 84 "B" 93) INFO:: Command: (setnum-from-serial-number 84 "B" 94) INFO:: Command: (insertion-code-from-serial-number 84 "B" 94) INFO:: Command: (setnum-from-serial-number 84 "B" 95) INFO:: Command: (insertion-code-from-serial-number 84 "B" 95) specs: 189 [[84, 'A', 1, ''], [84, 'A', 2, ''], [84, 'A', 3, ''], [84, 'A', 4, ''], [84, 'A', 5, ''], [84, 'A', 6, ''], [84, 'A', 7, ''], [84, 'A', 8, ''], [84, 'A', 9, ''], [84, 'A', 10, ''], [84, 'A', 11, ''], [84, 'A', 12, ''], [84, 'A', 13, ''], [84, 'A', 14, ''], [84, 'A', 15, ''], [84, 'A', 16, ''], [84, 'A', 17, ''], [84, 'A', 18, ''], [84, 'A', 19, ''], [84, 'A', 20, ''], [84, 'A', 21, ''], [84, 'A', 22, ''], [84, 'A', 23, ''], [84, 'A', 24, ''], [84, 'A', 25, ''], [84, 'A', 26, ''], [84, 'A', 27, ''], [84, 'A', 28, ''], [84, 'A', 29, ''], [84, 'A', 30, ''], [84, 'A', 31, ''], [84, 'A', 32, ''], [84, 'A', 33, ''], [84, 'A', 34, ''], [84, 'A', 35, ''], [84, 'A', 36, ''], [84, 'A', 37, ''], [84, 'A', 38, ''], [84, 'A', 39, ''], [84, 'A', 40, ''], [84, 'A', 41, ''], [84, 'A', 42, ''], [84, 'A', 43, ''], [84, 'A', 44, ''], [84, 'A', 45, ''], [84, 'A', 46, ''], [84, 'A', 47, ''], [84, 'A', 48, ''], [84, 'A', 49, ''], [84, 'A', 50, ''], [84, 'A', 51, ''], [84, 'A', 52, ''], [84, 'A', 53, ''], [84, 'A', 54, ''], [84, 'A', 55, ''], [84, 'A', 56, ''], [84, 'A', 57, ''], [84, 'A', 58, ''], [84, 'A', 59, ''], [84, 'A', 60, ''], [84, 'A', 61, ''], [84, 'A', 62, ''], [84, 'A', 63, ''], [84, 'A', 64, ''], [84, 'A', 65, ''], [84, 'A', 66, ''], [84, 'A', 67, ''], [84, 'A', 68, ''], [84, 'A', 69, ''], [84, 'A', 70, ''], [84, 'A', 71, ''], [84, 'A', 72, ''], [84, 'A', 73, ''], [84, 'A', 74, ''], [84, 'A', 75, ''], [84, 'A', 76, ''], [84, 'A', 77, ''], [84, 'A', 78, ''], [84, 'A', 79, ''], [84, 'A', 80, ''], [84, 'A', 81, ''], [84, 'A', 82, ''], [84, 'A', 83, ''], [84, 'A', 84, ''], [84, 'A', 85, ''], [84, 'A', 86, ''], [84, 'A', 87, ''], [84, 'A', 88, ''], [84, 'A', 89, ''], [84, 'A', 90, ''], [84, 'A', 91, ''], [84, 'A', 92, ''], [84, 'A', 93, ''], [84, 'B', 1, ''], [84, 'B', 2, ''], [84, 'B', 3, ''], [84, 'B', 4, ''], [84, 'B', 5, ''], [84, 'B', 6, ''], [84, 'B', 7, ''], [84, 'B', 8, ''], [84, 'B', 9, ''], [84, 'B', 10, ''], [84, 'B', 11, ''], [84, 'B', 12, ''], [84, 'B', 13, ''], [84, 'B', 14, ''], [84, 'B', 15, ''], [84, 'B', 16, ''], [84, 'B', 17, ''], [84, 'B', 18, ''], [84, 'B', 19, ''], [84, 'B', 20, ''], [84, 'B', 21, ''], [84, 'B', 22, ''], [84, 'B', 23, ''], [84, 'B', 24, ''], [84, 'B', 25, ''], [84, 'B', 26, ''], [84, 'B', 27, ''], [84, 'B', 28, ''], [84, 'B', 29, ''], [84, 'B', 30, ''], [84, 'B', 31, ''], [84, 'B', 32, ''], [84, 'B', 33, ''], [84, 'B', 34, ''], [84, 'B', 35, ''], [84, 'B', 36, ''], [84, 'B', 37, ''], [84, 'B', 38, ''], [84, 'B', 39, ''], [84, 'B', 40, ''], [84, 'B', 41, ''], [84, 'B', 42, ''], [84, 'B', 43, ''], [84, 'B', 44, ''], [84, 'B', 45, ''], [84, 'B', 46, ''], [84, 'B', 47, ''], [84, 'B', 48, ''], [84, 'B', 49, ''], [84, 'B', 50, ''], [84, 'B', 51, ''], [84, 'B', 52, ''], [84, 'B', 53, ''], [84, 'B', 54, ''], [84, 'B', 55, ''], [84, 'B', 56, ''], [84, 'B', 57, ''], [84, 'B', 58, ''], [84, 'B', 59, ''], [84, 'B', 60, ''], [84, 'B', 61, ''], [84, 'B', 62, ''], [84, 'B', 63, ''], [84, 'B', 64, ''], [84, 'B', 65, ''], [84, 'B', 66, ''], [84, 'B', 67, ''], [84, 'B', 68, ''], [84, 'B', 69, ''], [84, 'B', 70, ''], [84, 'B', 71, ''], [84, 'B', 72, ''], [84, 'B', 73, ''], [84, 'B', 74, ''], [84, 'B', 75, ''], [84, 'B', 76, ''], [84, 'B', 77, ''], [84, 'B', 78, ''], [84, 'B', 79, ''], [84, 'B', 80, ''], [84, 'B', 81, ''], [84, 'B', 82, ''], [84, 'B', 83, ''], [84, 'B', 84, ''], [84, 'B', 85, ''], [84, 'B', 86, ''], [84, 'B', 87, ''], [84, 'B', 88, ''], [84, 'B', 89, ''], [84, 'B', 90, ''], [84, 'B', 91, ''], [84, 'B', 92, ''], [84, 'B', 93, ''], [84, 'B', 94, ''], [84, 'B', 95, ''], [84, '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 Symmetry available for this molecule INFO:: NCS chain comparison 10/85 Molecule 85 read successfully DEBUG:: there were 7 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "GDP" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GDP.cif INFO:: using standard CCP4 Refmac dictionary to search for "Gr" INFO:: using standard CCP4 Refmac dictionary to search for "Ar" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif INFO:: using standard CCP4 Refmac dictionary to search for "Ur" INFO:: using standard CCP4 Refmac dictionary to search for "Cr" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif INFO:: using standard CCP4 Refmac dictionary to search for "OMC" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/o/OMC.cif INFO:: using standard CCP4 Refmac dictionary to search for "5BU" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/5/5BU.cif making spec from B 14 :: making spec from B 15 :: 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 Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 86 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 2 CB 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 Symmetry available for this molecule 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_Mon_Aug_31_16:14:03_2015_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 87 "A" 10 20 -55) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:03_2015_modification_1.pdb.gz INFO:: Command: (renumber-residue-range 87 "A" 90 93 10) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:03_2015_modification_2.pdb.gz INFO:: Command: (renumber-residue-range 87 "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 87 "A" 80 91 12) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:03_2015_modification_3.pdb.gz INFO:: Command: (renumber-residue-range 87 "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:: chain has 2 residues Symmetry available for this molecule Molecule 88 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:: chain has 2 residues Symmetry available for this molecule Molecule 89 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:: chain has 121 residues Symmetry available for this molecule Molecule 90 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/insulin.res") ll: 24 DEBUG:: space group initialised with symbol "I 21 3" in read_data_sm_cif() cell is Cell (77.726,77.726,77.726, 90, 90, 90) in read_data_sm_cif() spg is I 21 3 in read_data_sm_cif() reso is 0.588943 Map statistics: mean: -5.07006e-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 -0.00926962 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 1 6.16482 0 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 -0.00723863 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 ... Symmetry available for this molecule 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 ... Symmetry available for this molecule INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Masking around 32 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. B 2021 ALA N :: xyz = ( -11.33, 19.47, 57.91) B 2021 ALA C :: xyz = ( -12.04, 20.27, 60.12) B 2021 ALA CA :: xyz = ( -11.37, 20.62, 58.8) B 2021 ALA O :: xyz = ( -11.44, 20.43, 61.19) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Mon_Aug_31_16:14:04_2015_modification_0.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CD2" INFO:: Command: (add-terminal-residue 94 "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_Mon_Aug_31_16:14:04_2015_modification_0.res 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 90 "D" 68) INFO:: Command: (setnum-from-serial-number 90 "D" 68) INFO:: Command: (insertion-code-from-serial-number 90 "D" 68) ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... INFO:: Command: (n-chains 90) 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_Mon_Aug_31_16:14:04_2015_modification_1.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O " INFO:: Adding to solvent chain: D INFO:: Command: (n-chains 90) INFO:: Command: (resname-from-serial-number 90 "D" 96) INFO:: Command: (setnum-from-serial-number 90 "D" 96) INFO:: Command: (insertion-code-from-serial-number 90 "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:: chain has 5 residues Symmetry available for this molecule Molecule 95 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/miller/shelx-test4-NPD-mini.res") INFO:: Command: (close-molecule 95) ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... INFO:: Command: (close-molecule 91) INFO:: Command: (close-molecule 90) 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:: chain has 23 residues Symmetry available for this molecule Molecule 96 read successfully INFO:: Command: (read-shelx-ins-file "/home/paule/data/greg-data/horma-p21.res") 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 INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 97 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:: chain has 4 residues Symmetry available for this molecule Molecule 98 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:: chain has 4 residues Symmetry available for this molecule Molecule 99 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 Symmetry available for this molecule Molecule 100 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "3GP" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/3/3GP.cif 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_Mon_Aug_31_16:14:05_2015_modification_0.pdb.gz There are 2 data in coot-ccp4/libcheck_3GP.cif Welcome to Coot INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Mon_Aug_31_16:14:05_2015_modification_1.pdb.gz INFO:: Command: (delete-residue-hydrogens 100 "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 Symmetry available for this molecule Molecule 101 read successfully DEBUG:: there were 0 types with no dictionary here 1 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 No Symmetry for this model Molecule 102 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 No Symmetry for this model Molecule 103 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LIG" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIG.cif 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_Mon_Aug_31_16:14:05_2015_modification_2.pdb.gz INFO:: Command: (backup-state 100) INFO:: Command: (turn-off-backup 100) No graphics! Can't make Map Selection dialog. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:15030): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Command: (turn-on-backup 100) 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 Symmetry available for this molecule Molecule 104 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: Command: (copy-molecule 104) Symmetry available for this molecule INFO:: Command: (copy-molecule 104) Symmetry available for this molecule INFO:: Command: (copy-molecule 104) Symmetry available for this molecule INFO:: Command: (copy-molecule 104) Symmetry available for this molecule INFO:: Command: (copy-molecule 104) 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 Symmetry available for this molecule 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 110 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:: 0.146 seconds to read MTZ file INFO:: 0.091 seconds to initialize map INFO:: 0.067 seconds for FFT INFO:: 0.014 seconds for statistics Map mean: ........ -8.79003e-07 Map sigma: ....... 0.171188 Map maximum: ..... 1.34304 Map minimum: ..... -0.695441 INFO:: 0.007 seconds for contour map INFO:: 0.325 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:: 0.088 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.065 seconds for FFT INFO:: 0.017 seconds for statistics Map mean: ........ 2.0939e-06 Map sigma: ....... 0.0333923 Map maximum: ..... 0.366077 Map minimum: ..... -0.191665 INFO:: 0.003 seconds for contour map INFO:: 0.174 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) Executing ligand search... INFO:: ligand number 0 is molecule number 104 with wiggly flag: 0 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 102888 -0.0249776 143000 0.0112636 471775 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 6 0.77233 1 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 4.04177 and 4 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.0066 and 9 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.09237 and 4 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.85663 and 6 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.38681 and 10 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.61147 and 8 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.10047 and 8 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.69083 and 7 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.12333 and 2 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.84146 and 6 are decent out of 12 Symmetry available for this molecule Fitting NPO gave these results: [114, 115, 116, 117, 118, 119, 120, 121, 122, 123] 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 Symmetry available for this molecule Molecule 124 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: Command: (copy-molecule 124) INFO:: Command: (set-go-to-atom-molecule 124) INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_Aug_31_16:14:17_2015_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. distance: 4.32896043016 INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_Aug_31_16:14:17_2015_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_Aug_31_16:14:17_2015_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_Aug_31_16:14:17_2015_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. distance d2: 1.34544081022e-07 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 No Symmetry for this model Molecule 126 read successfully DEBUG:: there were 0 types with no dictionary making spec from A 1 :: making spec from A 2 :: making spec from A 3 :: 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 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 Symmetry available for this molecule 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 127 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 127 INFO:: Command: (assign-pir-sequence 127 "A" ">test ACDEFGHIKLMNPQ*") debug seq ACDEFGHIKLMNPQ storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 127 INFO:: Command: (assign-pir-sequence 127 "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 Symmetry available for this molecule INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 128 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:: 0.029 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.015 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.015 seconds for contour map INFO:: 0.062 seconds in total storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 128 INFO:: Command: (assign-pir-sequence 128 "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 128 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_Mon_Aug_31_16:14:18_2015_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 No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Aug_31_16:14:19_2015_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: Command: (copy-molecule 130) 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 131) INFO:: Command: (chain_id 131 0) INFO:: Command: (chain_id 131 1) INFO:: Command: (is-solvent-chain-p 131 "A") There are 8 residues in chain A INFO:: Command: (resname-from-serial-number 131 "A" 0) INFO:: Command: (setnum-from-serial-number 131 "A" 0) INFO:: Command: (insertion-code-from-serial-number 131 "A" 0) INFO:: Command: (resname-from-serial-number 131 "A" 1) INFO:: Command: (setnum-from-serial-number 131 "A" 1) INFO:: Command: (insertion-code-from-serial-number 131 "A" 1) INFO:: Command: (resname-from-serial-number 131 "A" 2) INFO:: Command: (setnum-from-serial-number 131 "A" 2) INFO:: Command: (insertion-code-from-serial-number 131 "A" 2) INFO:: Command: (resname-from-serial-number 131 "A" 3) INFO:: Command: (setnum-from-serial-number 131 "A" 3) INFO:: Command: (insertion-code-from-serial-number 131 "A" 3) INFO:: Command: (resname-from-serial-number 131 "A" 4) INFO:: Command: (setnum-from-serial-number 131 "A" 4) INFO:: Command: (insertion-code-from-serial-number 131 "A" 4) INFO:: Command: (resname-from-serial-number 131 "A" 5) INFO:: Command: (setnum-from-serial-number 131 "A" 5) INFO:: Command: (insertion-code-from-serial-number 131 "A" 5) INFO:: Command: (resname-from-serial-number 131 "A" 6) INFO:: Command: (setnum-from-serial-number 131 "A" 6) INFO:: Command: (insertion-code-from-serial-number 131 "A" 6) INFO:: Command: (resname-from-serial-number 131 "A" 7) INFO:: Command: (setnum-from-serial-number 131 "A" 7) INFO:: Command: (insertion-code-from-serial-number 131 "A" 7) INFO:: Command: (is-solvent-chain-p 131 "B") There are 8 residues in chain B INFO:: Command: (resname-from-serial-number 131 "B" 0) INFO:: Command: (setnum-from-serial-number 131 "B" 0) INFO:: Command: (insertion-code-from-serial-number 131 "B" 0) INFO:: Command: (resname-from-serial-number 131 "B" 1) INFO:: Command: (setnum-from-serial-number 131 "B" 1) INFO:: Command: (insertion-code-from-serial-number 131 "B" 1) INFO:: Command: (resname-from-serial-number 131 "B" 2) INFO:: Command: (setnum-from-serial-number 131 "B" 2) INFO:: Command: (insertion-code-from-serial-number 131 "B" 2) INFO:: Command: (resname-from-serial-number 131 "B" 3) INFO:: Command: (setnum-from-serial-number 131 "B" 3) INFO:: Command: (insertion-code-from-serial-number 131 "B" 3) INFO:: Command: (resname-from-serial-number 131 "B" 4) INFO:: Command: (setnum-from-serial-number 131 "B" 4) INFO:: Command: (insertion-code-from-serial-number 131 "B" 4) INFO:: Command: (resname-from-serial-number 131 "B" 5) INFO:: Command: (setnum-from-serial-number 131 "B" 5) INFO:: Command: (insertion-code-from-serial-number 131 "B" 5) INFO:: Command: (resname-from-serial-number 131 "B" 6) INFO:: Command: (setnum-from-serial-number 131 "B" 6) INFO:: Command: (insertion-code-from-serial-number 131 "B" 6) INFO:: Command: (resname-from-serial-number 131 "B" 7) INFO:: Command: (setnum-from-serial-number 131 "B" 7) INFO:: Command: (insertion-code-from-serial-number 131 "B" 7) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: Command: (copy-molecule 130) INFO:: Matching/moving molecule number 132 to 132 INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 2.51304e-06 rms devi: 2.68088e-06 max devi: 4.30027e-06 min devi: 5.3397e-07 INFO:: Axis orientation: ( 0.04358, -0.8724, 0.4869) INFO:: Rotation in CCP4 Polar Angles: Polar = ( 0, 0, 0) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Mon_Aug_31_16:14:19_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 1,-2.158e-08,-3.866e-08| | 2.158e-08, 1,-1.931e-09| | 3.866e-08, 1.931e-09, 1| ( -24.05, -24.05, -24.05) 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 Symmetry available for this molecule Molecule 133 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 Symmetry available for this molecule 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 134 read successfully DEBUG:: there were 2 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "CL" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CL.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAP" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAP.cif 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 133) INFO:: Command: (graphics-to-ca-plus-ligands-representation 134) INFO:: reference 133 has 750 atoms selected INFO:: moving 134 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance(/A) A 6 A 7 A 8 <---> A 2 : 0.7510 A 9 <---> A 3 : 0.9422 A 10 <---> A 4 : 0.6300 A 11 <---> A 5 : 0.7119 A 12 <---> A 6 : 0.6310 A 13 <---> A 7 : 0.4675 A 14 <---> A 8 : 0.4264 A 15 <---> A 9 : 0.9792 A 16 <---> A 10 : 0.7549 A 17 <---> A 11 : 0.4884 A 18 <---> A 12 : 0.7451 A 19 <---> A 13 : 0.4606 A 20 <---> A 14 : 1.2809 A 21 <---> A 15 : 1.2412 A 22 <---> A 16 : 1.0733 A 23 <---> A 17 : 0.9730 A 24 <---> A 18 : 0.4705 A 25 <---> A 19 : 0.3560 A 26 <---> A 20 : 3.1145 A 27 A 28 <---> A 21 : 1.5754 A 29 <---> A 22 : 1.6322 A 30 A 31 <---> A 23 : 1.9973 A 32 <---> A 25 : 1.8324 A 33 <---> A 26 : 0.9310 A 34 <---> A 27 : 0.6808 A 35 <---> A 28 : 0.2674 A 36 <---> A 29 : 0.5995 A 37 <---> A 30 : 0.6992 A 38 <---> A 31 : 0.8620 A 39 <---> A 32 : 0.8421 A 40 <---> A 33 : 0.7208 A 41 <---> A 34 : 0.8681 A 42 <---> A 35 : 0.7781 A 43 <---> A 36 : 0.6211 A 44 <---> A 37 : 0.4657 A 45 <---> A 38 : 0.7475 A 46 <---> A 39 : 0.5170 A 47 <---> A 40 : 0.5058 A 48 <---> A 41 : 0.8897 A 49 <---> A 42 : 0.5835 A 50 <---> A 43 : 0.4347 A 51 <---> A 44 : 0.6192 A 52 <---> A 45 : 0.2150 A 53 <---> A 46 : 0.7474 A 54 <---> A 47 : 1.0213 A 55 <---> A 48 : 0.9208 A 56 <---> A 49 : 0.9392 A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 0.4666 A 66 <---> A 61 : 0.0523 A 67 <---> A 62 : 1.0719 A 68 <---> A 63 : 0.7933 A 69 <---> A 64 : 0.8916 A 70 <---> A 65 : 1.2580 A 71 <---> A 66 : 0.6932 A 72 <---> A 67 : 1.0345 A 73 <---> A 68 : 1.4417 A 74 <---> A 69 : 0.9092 A 75 <---> A 70 : 1.6166 A 76 <---> A 71 : 0.8741 A 77 <---> A 72 : 0.2388 A 78 <---> A 73 : 0.3118 A 79 <---> A 74 : 0.3887 A 80 <---> A 75 : 0.7613 A 81 <---> A 76 : 0.9044 A 82 <---> A 77 : 0.6090 A 83 <---> A 78 : 1.7978 A 84 <---> A 79 : 1.9256 A 85 <---> A 80 : 1.3416 A 86 <---> A 81 : 0.5658 A 87 <---> A 82 : 0.4480 A 88 <---> A 83 : 0.9078 A 89 <---> A 84 : 0.3625 A 90 <---> A 85 : 0.4040 A 91 <---> A 86 : 0.4586 A 92 <---> A 87 : 0.4340 A 93 <---> A 88 : 0.3664 A 94 <---> A 89 : 0.4921 A 95 <---> A 90 : 0.6498 A 96 <---> A 91 : 1.5805 A 97 <---> A 92 : 2.8839 A 98 A 99 A 100 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI INFO:: backup file coot-backup/_home_paule_data_greg-data_1yb5.pdb_Mon_Aug_31_16:14:20_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal 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 42 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 43 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 44 averaged-map 45 difference-map INFO:: Command: (molecule-name 46) 46 /home/paule/data/greg-data/multi-carbo-coot-2.pdb INFO:: Command: (molecule-name 47) 47 /home/paule/data/greg-data/monomer-VAL.pdb INFO:: Command: (molecule-name 48) 48 /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb INFO:: Command: (molecule-name 49) 49 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 50) 50 /home/paule/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 51) 51 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 52) 52 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 53) 53 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 54) 54 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 55) 55 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 56) 56 /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb INFO:: Command: (molecule-name 57) 57 /home/paule/data/greg-data/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/pdb3hfl.ent 60 /home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT INFO:: Command: (molecule-name 61) 61 Ideal-A-form-RNA INFO:: Command: (molecule-name 62) 62 Ideal-A-form-RNA INFO:: Command: (molecule-name 63) 63 Ideal-A-form-DNA INFO:: Command: (molecule-name 64) 64 Ideal-A-form-DNA INFO:: Command: (molecule-name 65) 65 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 66) 66 /home/paule/data/greg-data/some-waters-with-ter.pdb INFO:: Command: (molecule-name 67) 67 /home/paule/data/greg-data/tm+some-waters.pdb INFO:: Command: (molecule-name 68) 68 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 69) 69 /home/paule/data/greg-data/water-test-no-cell.pdb INFO:: Command: (molecule-name 70) 70 /home/paule/data/greg-data/pathological-water-test.pdb INFO:: Command: (molecule-name 71) 71 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb 72 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 73) 73 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 74) 74 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 75) 75 /home/paule/data/greg-data/pdb1hvv.ent INFO:: Command: (molecule-name 76) 76 /home/paule/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 77) 77 /home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 78) 78 SymOp_-X,-X+Y,-Z+1/3_Copy_of_75 INFO:: Command: (molecule-name 79) 79 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 80) 80 Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 81) 81 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 82) 82 /home/paule/data/greg-data/pdb1py3.ent INFO:: Command: (molecule-name 83) 83 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 84) 84 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 85) 85 /home/paule/data/greg-data/2goz-manip.pdb INFO:: Command: (molecule-name 86) 86 rnase_zip_test.pdb.gz 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/HOF.RES INFO:: Command: (molecule-name 89) 89 /home/paule/data/greg-data/hollander.ins 92 /home/paule/data/greg-data/insulin.fcf INFO:: Command: (molecule-name 93) 93 atom selection from insulin.res INFO:: Command: (molecule-name 94) 94 atom selection from insulin.res INFO:: Command: (molecule-name 96) 96 /home/paule/data/greg-data/horma-p21.res INFO:: Command: (molecule-name 97) 97 new-horma.ins INFO:: Command: (molecule-name 98) 98 /home/paule/data/greg-data/crash.hat INFO:: Command: (molecule-name 99) 99 /home/paule/data/greg-data/crash.hat INFO:: Command: (molecule-name 100) 100 coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 101) 101 /home/paule/data/greg-data/monomer-3GP.pdb INFO:: Command: (molecule-name 102) 102 /home/paule/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 103) 103 /home/paule/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 104) 104 /home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 105) 105 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 106) 106 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 107) 107 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 108) 108 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 109) 109 Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 110) 110 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb 111 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT 112 /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT 113 Masked (by protein) INFO:: Command: (molecule-name 114) 114 Fitted ligand #0-0 INFO:: Command: (molecule-name 115) 115 Fitted ligand #1-0 INFO:: Command: (molecule-name 116) 116 Fitted ligand #2-0 INFO:: Command: (molecule-name 117) 117 Fitted ligand #3-0 INFO:: Command: (molecule-name 118) 118 Fitted ligand #4-0 INFO:: Command: (molecule-name 119) 119 Fitted ligand #5-0 INFO:: Command: (molecule-name 120) 120 Fitted ligand #6-0 INFO:: Command: (molecule-name 121) 121 Fitted ligand #7-0 INFO:: Command: (molecule-name 122) 122 Fitted ligand #8-0 INFO:: Command: (molecule-name 123) 123 Fitted ligand #9-0 INFO:: Command: (molecule-name 124) 124 coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 125) 125 Copy_of_coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 126) 126 /home/paule/data/greg-data/dipole-residues.pdb INFO:: Command: (molecule-name 127) 127 /home/paule/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 128) 128 /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb 129 /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 130) 130 Ideal-A-form-RNA INFO:: Command: (molecule-name 131) 131 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 132) 132 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 133) 133 /home/paule/data/greg-data/1wly.pdb INFO:: Command: (molecule-name 134) 134 /home/paule/data/greg-data/1yb5.pdb INFO:: Command: (graphics-to-ca-plus-ligands-representation 134) 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 Symmetry available for this molecule Molecule 135 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LGF" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LGF.cif 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 Symmetry available for this molecule INFO:: NCS chain comparison 0/337 Molecule 136 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LIE" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIE.cif INFO:: reference 135 has 169 atoms selected INFO:: moving 136 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_home_paule_data_greg-data_2gtn.pdb_Mon_Aug_31_16:14:21_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal 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:: 0.0290 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0150 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:: 0.0140 seconds for contour map INFO:: 0.0610 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:: 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 1 2.3885 1 INFO:: installing ghost map with name :Map 137 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 1 2.3885 1 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:: chain has 121 residues Symmetry available for this molecule Molecule 142 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 Symmetry available for this molecule 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 143 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:22_2015_modification_0.pdb.gz INFO:: Command: (delete-residue 143 "B" 1 "") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:22_2015_modification_1.pdb.gz INFO:: Command: (delete-residue 143 "B" 2 "") INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:22_2015_modification_2.pdb.gz INFO:: Command: (delete-residue 143 "B" 3 "") %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() 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: 143 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 143 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:22_2015_modification_3.pdb.gz INFO:: Command: (setnum-from-serial-number 143 "B" 0) INFO:: Command: (setnum-from-serial-number 143 "B" 1) INFO:: Command: (setnum-from-serial-number 143 "B" 2) INFO:: Command: (setnum-from-serial-number 143 "B" 3) INFO:: Command: (setnum-from-serial-number 143 "B" 4) INFO:: Command: (setnum-from-serial-number 143 "B" 5) INFO:: Command: (setnum-from-serial-number 143 "B" 6) INFO:: Command: (setnum-from-serial-number 143 "B" 7) INFO:: Command: (setnum-from-serial-number 143 "B" 8) INFO:: Command: (setnum-from-serial-number 143 "B" 9) INFO:: Command: (setnum-from-serial-number 143 "B" 10) INFO:: Command: (setnum-from-serial-number 143 "B" 11) INFO:: Command: (setnum-from-serial-number 143 "B" 12) INFO:: Command: (setnum-from-serial-number 143 "B" 13) INFO:: Command: (setnum-from-serial-number 143 "B" 14) INFO:: Command: (setnum-from-serial-number 143 "B" 15) INFO:: Command: (setnum-from-serial-number 143 "B" 16) INFO:: Command: (setnum-from-serial-number 143 "B" 17) INFO:: Command: (setnum-from-serial-number 143 "B" 18) INFO:: Command: (setnum-from-serial-number 143 "B" 19) INFO:: Command: (setnum-from-serial-number 143 "B" 20) INFO:: Command: (setnum-from-serial-number 143 "B" 21) INFO:: Command: (setnum-from-serial-number 143 "B" 22) INFO:: Command: (setnum-from-serial-number 143 "B" 23) INFO:: Command: (setnum-from-serial-number 143 "B" 24) INFO:: Command: (setnum-from-serial-number 143 "B" 25) INFO:: Command: (setnum-from-serial-number 143 "B" 26) INFO:: Command: (setnum-from-serial-number 143 "B" 27) INFO:: Command: (setnum-from-serial-number 143 "B" 28) INFO:: Command: (setnum-from-serial-number 143 "B" 29) INFO:: Command: (setnum-from-serial-number 143 "B" 30) INFO:: Command: (setnum-from-serial-number 143 "B" 31) INFO:: Command: (setnum-from-serial-number 143 "B" 32) INFO:: Command: (setnum-from-serial-number 143 "B" 33) INFO:: Command: (setnum-from-serial-number 143 "B" 34) INFO:: Command: (setnum-from-serial-number 143 "B" 35) INFO:: Command: (setnum-from-serial-number 143 "B" 36) INFO:: Command: (setnum-from-serial-number 143 "B" 37) INFO:: Command: (setnum-from-serial-number 143 "B" 38) INFO:: Command: (setnum-from-serial-number 143 "B" 39) INFO:: Command: (setnum-from-serial-number 143 "B" 40) INFO:: Command: (setnum-from-serial-number 143 "B" 41) INFO:: Command: (setnum-from-serial-number 143 "B" 42) INFO:: Command: (setnum-from-serial-number 143 "B" 43) INFO:: Command: (setnum-from-serial-number 143 "B" 44) INFO:: Command: (setnum-from-serial-number 143 "B" 45) INFO:: Command: (setnum-from-serial-number 143 "B" 46) INFO:: Command: (setnum-from-serial-number 143 "B" 47) INFO:: Command: (setnum-from-serial-number 143 "B" 48) INFO:: Command: (setnum-from-serial-number 143 "B" 49) INFO:: Command: (setnum-from-serial-number 143 "B" 50) INFO:: Command: (setnum-from-serial-number 143 "B" 51) INFO:: Command: (setnum-from-serial-number 143 "B" 52) INFO:: Command: (setnum-from-serial-number 143 "B" 53) INFO:: Command: (setnum-from-serial-number 143 "B" 54) INFO:: Command: (setnum-from-serial-number 143 "B" 55) INFO:: Command: (setnum-from-serial-number 143 "B" 56) INFO:: Command: (setnum-from-serial-number 143 "B" 57) INFO:: Command: (setnum-from-serial-number 143 "B" 58) INFO:: Command: (setnum-from-serial-number 143 "B" 59) INFO:: Command: (setnum-from-serial-number 143 "B" 60) INFO:: Command: (setnum-from-serial-number 143 "B" 61) INFO:: Command: (setnum-from-serial-number 143 "B" 62) INFO:: Command: (setnum-from-serial-number 143 "B" 63) INFO:: Command: (setnum-from-serial-number 143 "B" 64) INFO:: Command: (setnum-from-serial-number 143 "B" 65) INFO:: Command: (setnum-from-serial-number 143 "B" 66) INFO:: Command: (setnum-from-serial-number 143 "B" 67) INFO:: Command: (setnum-from-serial-number 143 "B" 68) INFO:: Command: (setnum-from-serial-number 143 "B" 69) INFO:: Command: (setnum-from-serial-number 143 "B" 70) INFO:: Command: (setnum-from-serial-number 143 "B" 71) INFO:: Command: (setnum-from-serial-number 143 "B" 72) INFO:: Command: (setnum-from-serial-number 143 "B" 73) INFO:: Command: (setnum-from-serial-number 143 "B" 74) INFO:: Command: (setnum-from-serial-number 143 "B" 75) INFO:: Command: (setnum-from-serial-number 143 "B" 76) INFO:: Command: (setnum-from-serial-number 143 "B" 77) INFO:: Command: (setnum-from-serial-number 143 "B" 78) INFO:: Command: (setnum-from-serial-number 143 "B" 79) INFO:: Command: (setnum-from-serial-number 143 "B" 80) INFO:: Command: (setnum-from-serial-number 143 "B" 81) INFO:: Command: (setnum-from-serial-number 143 "B" 82) INFO:: Command: (setnum-from-serial-number 143 "B" 83) INFO:: Command: (setnum-from-serial-number 143 "B" 84) INFO:: Command: (setnum-from-serial-number 143 "B" 85) INFO:: Command: (setnum-from-serial-number 143 "B" 86) INFO:: Command: (setnum-from-serial-number 143 "B" 87) INFO:: Command: (setnum-from-serial-number 143 "B" 88) INFO:: Command: (setnum-from-serial-number 143 "B" 89) INFO:: Command: (setnum-from-serial-number 143 "B" 90) INFO:: Command: (setnum-from-serial-number 143 "B" 91) INFO:: Command: (setnum-from-serial-number 143 "B" 92) INFO:: Command: (setnum-from-serial-number 143 "B" 93) INFO:: Command: (setnum-from-serial-number 143 "B" 94) INFO:: Command: (setnum-from-serial-number 143 "B" 95) INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:22_2015_modification_4.pdb.gz INFO:: Command: (mutate 143 "A" 2 "" "TRP") DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 143 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 143 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Aug_31_16:14:22_2015_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 Symmetry available for this molecule 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 144 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_Aug_31_16:14:23_2015_modification_0.pdb.gz INFO:: Command: (mutate 144 "A" 50 "" "ASP") %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() 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 144 "B") DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 144 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 144 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_Aug_31_16:14:23_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_Aug_31_16:14:23_2015_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 Symmetry available for this molecule 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 145 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 145 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 Symmetry available for this molecule INFO:: Command: (copy-molecule 145) INFO:: Matching/moving molecule number 146 to 145 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Mon_Aug_31_16:14:24_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal 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 146 to 145 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_Mon_Aug_31_16:14:24_2015_modification_1.pdb.gz INFO:: coordinates transformed by orthonal 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 146 to 145 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_Mon_Aug_31_16:14:24_2015_modification_2.pdb.gz INFO:: coordinates transformed by orthonal 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 146) 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 46) INFO:: Command: (molecule-name 47) INFO:: Command: (molecule-name 48) INFO:: Command: (molecule-name 49) INFO:: Command: (molecule-name 50) 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 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 63) INFO:: Command: (molecule-name 64) 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 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 75) INFO:: Command: (molecule-name 76) 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 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 96) INFO:: Command: (molecule-name 97) INFO:: Command: (molecule-name 98) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 100) INFO:: Command: (molecule-name 101) 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 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 116) INFO:: Command: (molecule-name 117) INFO:: Command: (molecule-name 118) INFO:: Command: (molecule-name 119) 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 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 135) INFO:: Command: (molecule-name 136) INFO:: Command: (close-molecule 138) INFO:: Command: (close-molecule 140) INFO:: Command: (molecule-name 142) INFO:: Command: (molecule-name 143) INFO:: Command: (molecule-name 144) INFO:: Command: (molecule-name 145) 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 Symmetry available for this molecule 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 147 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:: 0.0370 seconds to read MTZ file INFO:: 0.0210 seconds to initialize map INFO:: 0.0250 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:: 0.0080 seconds for contour map INFO:: 0.0940 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 148 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 148 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 148 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 5946 0.3997 3628 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 148 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 148 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 148 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 5946 0.3997 3628 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 148 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 148 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 148 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 5946 0.3997 3628 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 46) INFO:: Command: (molecule-name 47) INFO:: Command: (molecule-name 48) INFO:: Command: (molecule-name 49) INFO:: Command: (molecule-name 50) 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 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 63) INFO:: Command: (molecule-name 64) 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 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 75) INFO:: Command: (molecule-name 76) 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 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 96) INFO:: Command: (molecule-name 97) INFO:: Command: (molecule-name 98) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 100) INFO:: Command: (molecule-name 101) 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 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 116) INFO:: Command: (molecule-name 117) INFO:: Command: (molecule-name 118) INFO:: Command: (molecule-name 119) 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 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 135) INFO:: Command: (molecule-name 136) INFO:: Command: (molecule-name 142) INFO:: Command: (molecule-name 143) INFO:: Command: (molecule-name 144) INFO:: Command: (molecule-name 145) INFO:: Command: (molecule-name 147) 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-2.pdb', '/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_75', '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/HOF.RES', '/home/paule/data/greg-data/hollander.ins', '/home/paule/data/greg-data/insulin.fcf', '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 137 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 148 NCS found from matching Chain B onto Chain A', 'Map 148 NCS found from matching Chain C onto Chain A', 'Map 148 NCS found from matching Chain D onto Chain A', 'Map 148 NCS average of Chain A type molecules', 'Map 148 NCS found from matching Chain B onto Chain A', 'Map 148 NCS found from matching Chain C onto Chain A', 'Map 148 NCS found from matching Chain D onto Chain A', 'Map 148 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_wiggly_ligands There are 2 data in /home/paule/data/greg-data/libcheck_BUA.cif get_monomer type: BUA This residue has 2 defined non-H torsions of which 2 are (non-const) rotatable and 2 are non-const and non-ring torsions FAIL: ms.size() != wiggly_ligand_n_samples 9 10 FAIL: test_wiggly_ligands ok ---------------------------------------------------------------------- Ran 120 tests in 43.788s 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) Simple Averaged maps ... ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... 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 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 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 120 tests in 43.788s OK Unitest skip does not exist! The following tests were skipped and marked as passed: Libcif horne 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 42) INFO:: Command: (close-molecule 43) 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 92) INFO:: Command: (close-molecule 93) INFO:: Command: (close-molecule 94) INFO:: Command: (close-molecule 96) INFO:: Command: (close-molecule 97) INFO:: Command: (close-molecule 98) INFO:: Command: (close-molecule 99) INFO:: Command: (close-molecule 100) INFO:: Command: (close-molecule 101) 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 139) INFO:: Command: (close-molecule 141) INFO:: Command: (close-molecule 142) INFO:: Command: (close-molecule 143) INFO:: Command: (close-molecule 144) 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 152) INFO:: Command: (close-molecule 153) INFO:: Command: (close-molecule 154) INFO:: Command: (close-molecule 155) INFO:: Command: (close-molecule 156) 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) DEBUG:: planar_peptide_restraint_state():: returning ifound 1 INFO:: Command: (stereo-mode-state) DEBUG:: planar_peptide_restraint_state():: returning ifound 1 INFO:: Command: (stereo-mode-state) INFO:: Command: (save-state) load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "redefine-functions.scm" load "json-reader.scm" load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" load "local-code.scm" load "hello.scm" Good afternoon Paul Emsley,,,. Welcome to Coot 0.8.2. load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "parse-pisa-xml.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "prodrg-import.scm" load "dictionary-generators.scm" load "jligand.scm" load "americanisms.scm" load "group-settings.scm" test_coot_python: coot test passed