testing with python unittest testing with python unittest currently we are here: /home/emsley/autobuild/building/pc_2015-09-05__T03_40_09/coot-0.8.3-pre /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/bin/coot --no-graphics --script python-tests/coot_unittest.py INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/ There are 142 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/AR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HOH.cif INFO:: Reading coordinate file: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Importing python module coot using command from coot import * INFO:: coot.py imported Running python script /home/emsley/autobuild/Linux-pc-pre-release-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 Morning None, Welcome to Coot. 0.8.3-pre (set-display-intro-string "Good Morning None, Welcome to Coot. 0.8.3-pre") 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 INFO:: loading preferences file /home/emsley/.coot-preferences/chain-colour-mode.py Running python script /home/emsley/.coot-preferences/chain-colour-mode.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/scheme (set-display-intro-string "Good morning Paul. Welcome to Coot") (set-display-lists-for-maps 0) INFO:: loading preferences file /home/emsley/.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 13.00) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 0) (set-idle-function-rotate-angle 1.00) INFO:: loading preferences file /home/emsley/.coot-preferences/enhanced-ligand.scm INFO:: loading preferences file /home/emsley/.coot-preferences/extra-keys.scm INFO:: loading preferences file /home/emsley/.coot-preferences/key-bindings.scm INFO:: loading preferences file /home/emsley/.coot-preferences/mogul-interface.scm INFO:: loading preferences file /home/emsley/.coot-preferences/morph-residues-gui.scm INFO:: loading preferences file /home/emsley/.coot-preferences/raster3d.scm INFO:: loading preferences file /home/emsley/.coot-preferences/test-fit-step.scm INFO:: loading preferences file /home/emsley/.coot-preferences/use-pyrogen.scm (filter-fileselection-filenames-state) (get-active-map-drag-flag) Loading ~/.coot...done. 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/emsley/ccp4 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 ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 ... WARNING:: Error reading /home/emsley/data/greg-data/2WF6.pdb closing molecule number -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:: 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:: Reading coordinate file: /home/emsley/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/emsley/data/greg-data/ins-code-fragment-pre.pdb has been read. 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:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Sat_Sep__5_04:45:59_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Sat_Sep__5_04:45:59_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Sat_Sep__5_04:45:59_2015_modification_2.pdb.gz pre and post ins codes: A pass: ['A', 68, '', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'A', ' CA '] pass: ['A', 68, '', ' CA '] pass: ['A', 66, '', ' CA '] 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:: making map from mtz filename /home/emsley/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:: 0.032 seconds to read MTZ file INFO:: 0.038 seconds to initialize map INFO:: 0.036 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.056 seconds for contour map INFO:: 0.17 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/emsley/data/greg-data/broken.mtz INFO:: not an mtz file: /home/emsley/data/greg-data/broken.mtz got status: () ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... INFO:: map sigmas 0.311500996351 False ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... INFO:: making conventional map from MTZ filename /home/emsley/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 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.026 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.054 seconds for contour map INFO:: 0.125 seconds in total ok test09_1 (__main__.PdbMtzTestFunctions) db-main makes mainchain ... WARNING:: Error reading . . is a directory. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. ERROR 42 READ: Duplicate sequence number and insertion code. LINE #868 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ka1.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 ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:46:00_2015_modification_0.pdb.gz 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:: backup file coot-backup/atom_selection_from_regression-test-terminal-residue.pdb_Sat_Sep__5_04:46:00_2015_modification_0.pdb.gz ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 Sphere mol: there are 4 residues in chain B Found 20 sphere atoms ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:01_2015_modification_0.pdb.gz residue info (should be False): False ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:46:01_2015_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:46:01_2015_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:46:01_2015_modification_2.pdb.gz ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/rotamer-test-fragment.pdb PDB file /home/emsley/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: Reading coordinate file: /home/emsley/data/greg-data/res098.pdb PDB file /home/emsley/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links 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): 3.097 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_res098.pdb_Sat_Sep__5_04:46:02_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: making map from mtz filename /home/emsley/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:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.06 seconds for contour map INFO:: 0.13 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:02_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! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:02_2015_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 12.0528 ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3knw.ent PDB file /home/emsley/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/e/EDO.cif INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3knw.ent_Sat_Sep__5_04:46:02_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:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links 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 INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1py3.ent_Sat_Sep__5_04:46:02_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:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: making map from mtz filename /home/emsley/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:: 0.026 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.053 seconds for contour map INFO:: 0.122 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:03_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 21 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-pepflip-test.pdb_Sat_Sep__5_04:46:03_2015_modification_0.pdb.gz flipped 65 A ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x95b67c0 omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:46:03_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:46:03_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_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:46:03_2015_modification_2.pdb.gz created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 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: 2093.85 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 73) at -4805.58 Final Estimated RMS Z Scores: bonds: 1.96376 angles: 1.36828 torsions: N/A planes: 3.39034 non-bonded: 1.57283 chiral vol: 0.269178 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.78 Refinement elapsed time: 0.014 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:46:03_2015_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:46:03_2015_modification_4.pdb.gz ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:46:03_2015_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.73212 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 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: -5944.23 Initial RMS Z values bonds: 1.42865 angles: 1.60187 torsions: N/A planes: 4.65152 non-bonded: 1.50738 chiral vol: 0.465999 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 54) at -6086.61 Final Estimated RMS Z Scores: bonds: 1.76717 angles: 1.20831 torsions: N/A planes: 3.56208 non-bonded: 0.682416 chiral vol: 0.097984 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 4.883 Refinement elapsed time: 0.017 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:46:03_2015_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: making map from mtz filename /home/emsley/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:: 0.026 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.053 seconds for contour map INFO:: 0.122 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: -2789.6 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 17) at -2928.54 Final Estimated RMS Z Scores: bonds: 1.16053 angles: 1.407 torsions: N/A planes: 1.81259 non-bonded: 3.14639 chiral vol: 0.814128 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.25 Refinement elapsed time: 0.007 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:04_2015_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. refined moved: d= 0.293867304294 ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:46:04_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 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: -10999.4 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 26) at -11214.5 Final Estimated RMS Z Scores: bonds: 1.06467 angles: 0.683775 torsions: N/A planes: 1.52937 non-bonded: 0.00163455 chiral vol: 0.245659 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.792 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:46:04_2015_modification_1.pdb.gz INFO:: replace_coords: 23 atoms updated. 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: -12774.1 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 -16169.7 Final Estimated RMS Z Scores: bonds: 1.66958 angles: 1.90732 torsions: N/A planes: 1.96529 non-bonded: 0.0081404 chiral vol: 1.8752 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.172 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:46:04_2015_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. ======= got bond length 1.29249295516 ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: making map from mtz filename /home/emsley/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:: 0.027 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.054 seconds for contour map INFO:: 0.124 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: -8698.52 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 9) at -11784.1 Final Estimated RMS Z Scores: bonds: 1.75016 angles: 2.1125 torsions: N/A planes: 2.16571 non-bonded: 0.0267538 chiral vol: 2.05521 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.66 Refinement elapsed time: 0.078 refinement results: ['', 0, [['Bonds', 'Bonds: 1.750', 1.7501633167266846], ['Angles', 'Angles: 2.112', 2.1124963760375977], ['Planes', 'Planes: 2.166', 2.1657142639160156], ['Non-bonded', 'Non-bonded: 0.164', 0.16356587409973145], ['Chirals', 'Chirals: 2.055', 2.0552055835723877]]] ow factor 2.02089488506 INFO:: setting refinement weight to 14.6914208943 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: -462.702 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 14) at -2710.3 Final Estimated RMS Z Scores: bonds: 0.543342 angles: 1.69214 torsions: N/A planes: 1.4437 non-bonded: 0.0110649 chiral vol: 1.26076 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.854 Refinement elapsed time: 0.193 refinement results: ['', 0, [['Bonds', 'Bonds: 0.543', 0.5433424115180969], ['Angles', 'Angles: 1.692', 1.6921378374099731], ['Planes', 'Planes: 1.444', 1.443696141242981], ['Non-bonded', 'Non-bonded: 0.105', 0.10518989711999893], ['Chirals', 'Chirals: 1.261', 1.260756492614746]]] ow factor 1.2349832207 INFO:: setting refinement weight to 9.63255898156 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: 456.856 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 16) at -1724.29 Final Estimated RMS Z Scores: bonds: 0.413261 angles: 1.64314 torsions: N/A planes: 1.22241 non-bonded: 0.00764731 chiral vol: 1.26139 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.415 Refinement elapsed time: 0.56 refinement results: ['', 0, [['Bonds', 'Bonds: 0.413', 0.41326120495796204], ['Angles', 'Angles: 1.643', 1.6431448459625244], ['Planes', 'Planes: 1.222', 1.222404956817627], ['Non-bonded', 'Non-bonded: 0.087', 0.08744888007640839], ['Chirals', 'Chirals: 1.261', 1.2613942623138428]]] ow factor 1.13505131751 INFO:: setting refinement weight to 7.47671240278 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: 848.728 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 70) at -1303.7 Final Estimated RMS Z Scores: bonds: 0.368577 angles: 1.62017 torsions: N/A planes: 1.11149 non-bonded: 0.00633804 chiral vol: 1.25538 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.893 Refinement elapsed time: 0.479 refinement results: ['', 0, [['Bonds', 'Bonds: 0.369', 0.3685774505138397], ['Angles', 'Angles: 1.620', 1.6201729774475098], ['Planes', 'Planes: 1.111', 1.111485242843628], ['Non-bonded', 'Non-bonded: 0.080', 0.07961183786392212], ['Chirals', 'Chirals: 1.255', 1.2553826570510864]]] ow factor 1.08890458196 ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/alt-conf-waters.pdb PDB file /home/emsley/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_alt-conf-waters.pdb_Sat_Sep__5_04:46:07_2015_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/backrub-fragment.pdb PDB file /home/emsley/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Sat_Sep__5_04:46:07_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Sat_Sep__5_04:46:07_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:: making map from mtz filename /home/emsley/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:: 0.03 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.053 seconds for contour map INFO:: 0.127 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:: Reading coordinate file: /home/emsley/data/greg-data/test-TER-OXT.pdb PDB file /home/emsley/data/greg-data/test-TER-OXT.pdb has been read. 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_emsley_data_greg-data_test-TER-OXT.pdb_Sat_Sep__5_04:46:08_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 WARNING:: This residue already has an OXT - aborting found TER TER 25 ASP A 14 ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/val.pdb PDB file /home/emsley/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_emsley_data_greg-data_val.pdb_Sat_Sep__5_04:46:08_2015_modification_0.pdb.gz ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/2yie-frag.pdb PDB file /home/emsley/data/greg-data/2yie-frag.pdb has been read. 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_emsley_data_greg-data_2yie-frag.pdb_Sat_Sep__5_04:46:08_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 ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/n/NCO.cif INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Sat_Sep__5_04:46:08_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 ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Sat_Sep__5_04:46:09_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 ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... failed to delete residue atoms A 88 :A: ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... INFO:: making map from mtz filename /home/emsley/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:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.047 seconds for contour map INFO:: 0.119 seconds in total INFO:: making map from mtz filename /home/emsley/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:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.039 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.046 seconds for contour map INFO:: 0.122 seconds in total INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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: -0.00140896 st.d: 0.305562 Map statistics: min: -0.921659, max: 3.05176 -0.871991 10 -0.772655 72 -0.67332 614 -0.573984 3970 -0.474649 16922 -0.375313 47064 -0.275978 80116 -0.176642 105930 -0.0773069 131011 0.0220286 142638 0.121364 80192 0.2207 37039 0.320035 20148 0.419371 14894 0.518706 11885 0.618042 10488 0.717377 8813 0.816713 7252 0.916048 5646 1.01538 4143 1.11472 2992 1.21405 2070 1.31339 1406 1.41273 857 1.51206 523 1.6114 288 1.71073 155 1.81007 64 1.9094 36 2.00874 17 2.10807 8 2.20741 2 2.30675 5 2.40608 4 2.50542 2 2.60475 1 2.70409 1 2.80342 1 2.90276 0 3.00209 1 3.10143 0 high-values: [0.8227398991584778, 1.0119965076446533, 1.0171315670013428, 1.0682491064071655, 0.7381036281585693, 0.8017536401748657, 0.6875786781311035, 0.6362036466598511, 1.0157028436660767, 0.9525023698806763, 0.9898293018341064] 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: -0.00140896 st.d: 0.0605043 Map statistics: min: -2.99276, max: 0.774316 -2.94567 2 -2.8515 2 -2.75732 1 -2.66314 2 -2.56896 3 -2.47479 3 -2.38061 1 -2.28643 4 -2.19226 4 -2.09808 3 -2.0039 4 -1.90973 4 -1.81555 6 -1.72137 12 -1.6272 20 -1.53302 21 -1.43884 29 -1.34466 47 -1.25049 87 -1.15631 85 -1.06213 153 -0.967957 182 -0.87378 266 -0.779603 331 -0.685426 378 -0.591249 415 -0.497072 517 -0.402895 588 -0.308718 704 -0.214541 858 -0.120364 1154 -0.0261874 723063 0.0679896 2120 0.162167 2190 0.256343 1772 0.35052 1353 0.444697 623 0.538874 215 0.633051 49 0.727228 9 0.821405 0 diff-high-values: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] diff-low-values: [-0.5536488890647888, -0.9707267880439758, -0.6932031512260437, -0.8488963842391968, -0.8271133303642273, -1.0860068798065186, -1.2907465696334839, -1.183866262435913, -0.9473038911819458, -0.893179178237915] ok test29_1 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... INFO:: making map from mtz filename /home/emsley/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:: 0.027 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.045 seconds for contour map INFO:: 0.114 seconds in total INFO:: making map from mtz filename /home/emsley/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:: 0.026 seconds to read MTZ file INFO:: 0.05 seconds to initialize map INFO:: 0.048 seconds for FFT INFO:: 0.012 seconds for statistics Map mean: ........ 1.16132e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.06 seconds for contour map INFO:: 0.196 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 160, 192, 96) by 1 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1 Map statistics: mean: -3.34695e-06 st.d: 0.311048 Map statistics: min: -0.916532, max: 3.05151 -0.866931 10 -0.76773 76 -0.668529 693 -0.569328 4378 -0.470127 18338 -0.370926 49769 -0.271725 82935 -0.172524 109167 -0.0733227 133898 0.0258783 127242 0.125079 79379 0.22428 36898 0.323482 20503 0.422683 15332 0.521884 12363 0.621085 10886 0.720286 9118 0.819487 7521 0.918688 5833 1.01789 4256 1.11709 3092 1.21629 2109 1.31549 1444 1.41469 867 1.51389 533 1.6131 302 1.7123 160 1.8115 68 1.9107 40 2.0099 20 2.1091 11 2.2083 7 2.3075 9 2.4067 5 2.5059 5 2.60511 4 2.70431 2 2.80351 4 2.90271 1 3.00191 2 3.10111 0 Map statistics: mean: 3.34818e-06 st.d: 0.00108591 Map statistics: min: -0.0109202, max: 0.00950789 -0.0106648 1 -0.0101541 4 -0.00964341 5 -0.00913271 7 -0.00862201 8 -0.00811131 17 -0.00760061 17 -0.00708991 20 -0.0065792 18 -0.0060685 43 -0.0055578 95 -0.0050471 231 -0.0045364 544 -0.0040257 1166 -0.00351499 2162 -0.00300429 4144 -0.00249359 8444 -0.00198289 16359 -0.00147219 32958 -0.000961487 73386 -0.000450785 158314 5.99161e-05 204518 0.000570618 125581 0.00108132 51957 0.00159202 23884 0.00210272 12695 0.00261342 7551 0.00312413 4844 0.00363483 3115 0.00414553 1977 0.00465623 1264 0.00516693 844 0.00567763 507 0.00618833 274 0.00669904 169 0.00720974 74 0.00772044 47 0.00823114 18 0.00874184 10 0.00925254 8 0.00976325 0 INFO:: map sigmas: normal 0.311048001051 and diff-map: 0.00108590547461 ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/multi-carbo-coot-2.pdb PDB file /home/emsley/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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/f/FUC.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/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): 12.955 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_multi-carbo-coot-2.pdb_Sat_Sep__5_04:46:12_2015_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. bond-length: 1.44034105603 ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-VAL.pdb PDB file /home/emsley/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 47 read successfully DEBUG:: there were 0 types with no dictionary 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): 13.624 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:46:12_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 47 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:46:12_2015_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:46:12_2015_modification_0.pdb.gz PDB file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:46:12_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 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): 13.68 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:46:12_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. ok test32_0 (__main__.PdbMtzTestFunctions) Test for mangling of hydrogen names from a PDB v 3.0 ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. 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): 14.622 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Sat_Sep__5_04:46:13_2015_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... looping over restraint Symmetry available for this molecule 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: 4022.89 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 45) at -473.751 Final Estimated RMS Z Scores: bonds: 0.439408 angles: 0.372208 torsions: N/A planes: 0.330586 non-bonded: 0.0266619 chiral vol: 0.129927 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 14.665 Refinement elapsed time: 0.023 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:46:13_2015_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. Bond-length: 2.83560581772 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: 3144.9 Initial RMS Z values bonds: 17.3729 angles: 0.372208 torsions: N/A planes: 0.330586 non-bonded: 0 chiral vol: 0.129927 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 4) at -541.998 Final Estimated RMS Z Scores: bonds: 0.134912 angles: 0.150558 torsions: N/A planes: 0.422347 non-bonded: 0 chiral vol: 0.0454846 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 14.696 Refinement elapsed time: 0.018 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:46:13_2015_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. OK plane atom CB Bond-length: 1.51508575348 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:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ACT.cif There are 2 data in /home/emsley/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: 5304.03 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 2) at -137.715 Final Estimated RMS Z Scores: bonds: 0.0324876 angles: 0.177004 torsions: N/A planes: 0.0487715 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 15.523 Refinement elapsed time: 0.042 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-ACT.pdb_Sat_Sep__5_04:46:14_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_2.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_3.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_6.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_7.pdb.gz ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... Symmetry available for this molecule Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:15_2015_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. 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:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 in new_molecule_by_residue_type_selection Something bad happened - No residues selected ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:16_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:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 Rotamer 0 : m-85 100.0 Rotamer 1 : t80 90.1668395996 Rotamer 2 : p90 50.7077865601 Rotamer 3 : m -30 21.4231548309 Rotamer 4 : m -30 21.4231548309 ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/emsley/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_emsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Sat_Sep__5_04:46:17_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: 4 "A" 1 ""] -> ASP [spec: 4 "A" 2 ""] -> VAL [spec: 4 "A" 3 ""] -> SER [spec: 4 "A" 11 ""] -> LEU [spec: 4 "A" 12 ""] -> PRO [spec: 4 "A" 13 ""] -> PRO [spec: 4 "A" 62 ""] -> PRO [spec: 4 "A" 63 ""] -> GLY Deletions: [spec: 4 "A" 24 ""] [spec: 4 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions ::::: [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:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:18_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:19_2015_modification_0.pdb.gz ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3hfl.ent PDB file /home/emsley/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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PCA.cif INFO:: making map from mtz filename /home/emsley/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:: 0.023 seconds to read MTZ file INFO:: 0.007 seconds to initialize map INFO:: 0.013 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 2.00384e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.01 seconds for contour map INFO:: 0.056 seconds in total INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Sat_Sep__5_04:46:19_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.83405 INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Sat_Sep__5_04:46:19_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_Sat_Sep__5_04:46:20_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Sat_Sep__5_04:46:20_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 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_Sat_Sep__5_04:46:20_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Sat_Sep__5_04:46:20_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 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_Sat_Sep__5_04:46:20_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 mutated base to type DC INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 mutated base to type DG INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 mutated base to type DA INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 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_Sat_Sep__5_04:46:20_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 mutated base to type Cd INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 mutated base to type Gd INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 mutated base to type Ad INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:46:20_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 mutated base to type Td ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... Symmetry available for this molecule INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:20_2015_modification_0.pdb.gz ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/some-waters-with-ter.pdb PDB file /home/emsley/data/greg-data/some-waters-with-ter.pdb has been read. 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:: backup file coot-backup/_home_emsley_data_greg-data_some-waters-with-ter.pdb_Sat_Sep__5_04:46:20_2015_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tm+some-waters.pdb PDB file /home/emsley/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 -0.0338214 stdev: 0.146177) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 1.5 3.6 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 28.11, 32.19, 9.322) is too big to be water INFO:: cluster at xyz = ( 70.02, 19.14, 18.63) is too big to be water INFO:: cluster at xyz = ( 52.69, 10.8, 11.54) is too big to be water INFO:: cluster at xyz = ( 73.3, 12.31, 14.45) is too big to be water INFO:: cluster at xyz = ( 39.77, 8.163, 19.52) is too big to be water INFO:: cluster at xyz = ( 53.3, -4.948, -2.745) is too big to be water INFO:: cluster at xyz = ( 40.96, 7.032, 16.25) is too big to be water INFO:: found 68 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tm+some-waters.pdb_Sat_Sep__5_04:46:21_2015_modification_0.pdb.gz INFO:: Adding to solvent chain: D ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:22_2015_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/water-test-no-cell.pdb PDB file /home/emsley/data/greg-data/water-test-no-cell.pdb has been read. 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_emsley_data_greg-data_water-test-no-cell.pdb_Sat_Sep__5_04:46:25_2015_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /home/emsley/data/greg-data/pathological-water-test.pdb PDB file /home/emsley/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_pathological-water-test.pdb_Sat_Sep__5_04:46:26_2015_modification_0.pdb.gz INFO:: moved 181 water molecules ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... Symmetry available for this molecule INFO:: making map from mtz filename /home/emsley/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:: 0.027 seconds to read MTZ file INFO:: 0.012 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.06932e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.022 seconds for contour map INFO:: 0.08 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:26_2015_modification_0.pdb.gz ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... Symmetry available for this molecule 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:26_2015_modification_0.pdb.gz ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TAR.cif INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 76 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/n/NPO.cif -------- starting chain list ----------- ['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 ['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K'] ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... Symmetry available for this molecule Symmetry available for this molecule 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:29_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:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links 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 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:31_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:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:32_2015_modification_0.pdb.gz 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:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 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:: Reading coordinate file: /home/emsley/data/greg-data/2goz-manip.pdb PDB file /home/emsley/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/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/emsley/ccp4/ccp4-6.5/ccp4-6.5/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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CR.cif INFO:: using standard CCP4 Refmac dictionary to search for "OMC" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/o/OMC.cif INFO:: using standard CCP4 Refmac dictionary to search for "5BU" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/5/5BU.cif making spec from B 14 :: making spec from B 15 :: gzip: stdout: Broken pipe gzip: stdout: Broken pipe 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:: 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 ok test999_0 (__main__.PdbMtzTestFunctions) Renumber residue range without overwriting coordinates. ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:35_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:35_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:35_2015_modification_2.pdb.gz WARNING:: the new residue range overlaps with original one. Please change the range. Nothing has been done. INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:35_2015_modification_3.pdb.gz ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... 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 ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... 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:: spacegroup: I 41 2 2 ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... 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 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: -5.07009e-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: -1.00547e-05 st.d: 0.0468085 Map statistics: min: -0.211523, max: 0.648623 -0.200772 7 -0.179268 48 -0.157764 209 -0.136261 787 -0.114757 2257 -0.0932533 5676 -0.0717496 12730 -0.050246 24380 -0.0287423 38191 -0.00723865 46229 0.014265 43880 0.0357687 32484 0.0572723 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 ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... Symmetry available for this molecule 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_Sat_Sep__5_04:46:36_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" ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Sat_Sep__5_04:46:36_2015_modification_0.res 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.305174 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: 1.5 3.6 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 126 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Sat_Sep__5_04:46:36_2015_modification_1.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O " INFO:: Adding to solvent chain: D ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... 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 ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... 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:: SHELXL file new-horma.ins written. 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 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 ... 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 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 ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/3/3GP.cif INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:46:36_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_Sat_Sep__5_04:46:36_2015_modification_1.pdb.gz ok test02_0 (__main__.LigandTestFunctions) Set Bond thickness test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links 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:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb PDB file /home/emsley/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:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb PDB file /home/emsley/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/emsley/ccp4/ccp4-6.5/ccp4-6.5/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:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:46:36_2015_modification_2.pdb.gz No graphics! Can't make Map Selection dialog. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 104 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links 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/emsley/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:: 0.148 seconds to read MTZ file INFO:: 0.105 seconds to initialize map INFO:: 0.078 seconds for FFT INFO:: 0.016 seconds for statistics Map mean: ........ -8.79008e-07 Map sigma: ....... 0.171188 Map maximum: ..... 1.34304 Map minimum: ..... -0.695441 INFO:: 0.009 seconds for contour map INFO:: 0.356 seconds in total INFO:: making difference map from MTZ filename /home/emsley/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:: 0.084 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.079 seconds for FFT INFO:: 0.015 seconds for statistics Map mean: ........ 2.09389e-06 Map sigma: ....... 0.0333923 Map maximum: ..... 0.366077 Map minimum: ..... -0.191665 INFO:: 0.004 seconds for contour map INFO:: 0.183 seconds in total Executing ligand search... INFO:: ligand number 0 is molecule number 104 with wiggly flag: 0 ligand eigen values: 1.92448 25.091 59.3276 ligand eigen vectors: | -0.4263, 0.8296, -0.3606| | -0.1625, 0.322, 0.9327| | 0.8899, 0.4562, -0.002469| 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 -0.0612188 102890 -0.0249776 142998 0.0112637 471775 0.0475049 106846 0.0837462 56087 0.119987 21597 0.156229 6911 0.19247 2135 0.228711 920 0.264952 467 0.301194 346 0.337435 216 0.373676 118 0.409917 117 0.446159 80 0.4824 50 0.518641 28 0.554882 33 0.591124 15 0.627365 14 0.663606 11 0.699847 2 0.736089 7 0.77233 0 INFO:: find_clusters map_rms is 0.171132 INFO:: Using density cut-off: 0.171132 (1 sigma) (mean -0.0216776 stdev: 0.0886191) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4 3.2 INFO:: Finding clusters...done There are 487 clusers Here are the top 10 clusers: Number: 0 # grid points: 114 score: 39.7226 | 0.002711, -0.8301, 0.5576| | 0.6324, -0.4305, -0.644| | 0.7746, 0.3544, 0.5238| ( 10.22, 41.14, 18.33) xyz = ( 1.249, 1.289, 1.099) eigenvalues: 36.1609 84.686 384.271 Number: 1 # grid points: 70 score: 16.5731 | -0.4748, -0.44, -0.7622| | -0.8071, -0.1276, 0.5765| | -0.3509, 0.8889, -0.2946| ( 36.54, 43.69, 42.89) xyz = ( 0.9048, 0.7209, 1.257) eigenvalues: 30.4656 130.385 43.3555 Number: 2 # grid points: 61 score: 15.166 | 0.7705, -0.1438, 0.621| | 0.5329, 0.6798, -0.5038| | -0.3497, 0.7191, 0.6005| ( 43.01, 6.792, 48.32) xyz = ( 1.124, 0.9864, 1.129) eigenvalues: 12.4072 22.17 179.601 Number: 3 # grid points: 38 score: 13.4201 | -0.6008, 0.4916, 0.6304| | 0.7975, 0.3146, 0.5148| | 0.05474, 0.812, -0.581| ( 43.41, 22.55, 50.71) xyz = ( 0.8263, 0.6495, 1.179) eigenvalues: 8.31569 73.3292 13.1548 Number: 4 # grid points: 36 score: 13.399 | -0.8278, -0.4676, 0.31| | -0.5603, 0.6618, -0.498| | 0.02776, -0.586, -0.8099| ( 2.361, 56.41, 25.04) xyz = ( 0.6151, 0.6609, 0.6501) eigenvalues: 11.5733 20.5705 12.4136 Number: 5 # grid points: 40 score: 12.4681 | 0.3772, 0.6453, 0.6643| | 0.9261, -0.2552, -0.2779| | -0.009792, 0.72, -0.6939| ( 46.97, 1.923, 47.25) xyz = ( 0.9152, 0.5897, 0.9478) eigenvalues: 9.79185 13.9394 59.6129 Number: 6 # grid points: 34 score: 12.3706 | -0.3425, -0.4238, 0.8385| | -0.9394, 0.1382, -0.3139| | 0.01716, -0.8952, -0.4454| ( 73.14, 32.61, 45.23) xyz = ( 0.7746, 0.5559, 0.6475) eigenvalues: 8.91241 11.7126 24.5384 Number: 7 # grid points: 40 score: 11.8091 | -0.6826, 0.6985, 0.2147| | -0.6946, -0.7115, 0.1066| | 0.2272, -0.07637, 0.9708| ( 15.51, 51.69, 27.48) xyz = ( 1.045, 1.06, 0.5268) eigenvalues: 8.09804 80.8051 10.8323 Number: 8 # grid points: 43 score: 11.6116 | -0.4261, 0.4445, -0.7879| | -0.8865, -0.3791, 0.2655| | -0.1806, 0.8116, 0.5556| ( 27.27, 53.9, 17.59) xyz = ( 1.027, 0.5894, 0.8771) eigenvalues: 9.65728 19.8066 63.8821 debug:: n_ligands_for_cluster() top_score 4.04177 and 4 are decent out of 12 Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.0066 and 4 are decent out of 12 Symmetry available for this molecule 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 Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.85663 and 3 are decent out of 12 Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.38681 and 4 are decent out of 12 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.61147 and 4 are decent out of 12 Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 2.10047 and 2 are decent out of 12 Symmetry available for this molecule Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.69083 and 2 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 Symmetry available for this molecule debug:: n_ligands_for_cluster() top_score 1.84146 and 5 are decent out of 12 Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Fitting NPO gave these results: [114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136] ok test07_0 (__main__.LigandTestFunctions) Flip residue (around eigen vectors) ... 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 137 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:46:48_2015_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. distance: 4.05825912267 INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:46:48_2015_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:46:48_2015_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:46:48_2015_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. distance d2: 1.60332907424e-07 ok test08_0 (__main__.LigandTestFunctions) Test dipole ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/dipole-residues.pdb PDB file /home/emsley/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 139 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/emsley/data/greg-data/libcheck_3GP.cif not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif not found. init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 140 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 140 debug seq ACDEFGHIKLMNPQ storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 140 ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb PDB file /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 141 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.026 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.06932e-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 storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 141 Cootaneering: imol 141 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_emsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Sat_Sep__5_04:46:51_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_Sat_Sep__5_04:46:52_2015_modification_0.pdb.gz !! Warning:: No symmetry available for this molecule No Symmetry for this model There are 8 residues in chain A There are 8 residues in chain B !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: Matching/moving molecule number 145 to 145 INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 2.51644e-06 rms devi: 2.66951e-06 max devi: 4.13099e-06 min devi: 7.20885e-07 INFO:: Axis orientation: ( 0.5603, -0.1206, 0.8194) INFO:: Rotation in CCP4 Polar Angles: Polar = ( 0, 0, 0) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Sat_Sep__5_04:46:53_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 1, -1.83e-08,-2.694e-09| | 1.83e-08, 1,-1.251e-08| | 2.694e-09, 1.251e-08, 1| ( -24.08, -24.08, -24.08) No unit cell for this molecule, hence no fractional matrix. ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/1wly.pdb PDB file /home/emsley/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 146 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/1yb5.pdb PDB file /home/emsley/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: Found 1 models Model 1 had 0 links 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 147 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CL.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAP" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/n/NAP.cif INFO:: reference 146 has 750 atoms selected INFO:: moving 147 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance(/A) A 6 A 7 A 8 <---> A 2 : 0.7510 A 9 <---> A 3 : 0.9422 A 10 <---> A 4 : 0.6300 A 11 <---> A 5 : 0.7119 A 12 <---> A 6 : 0.6310 A 13 <---> A 7 : 0.4675 A 14 <---> A 8 : 0.4264 A 15 <---> A 9 : 0.9792 A 16 <---> A 10 : 0.7549 A 17 <---> A 11 : 0.4884 A 18 <---> A 12 : 0.7451 A 19 <---> A 13 : 0.4606 A 20 <---> A 14 : 1.2809 A 21 <---> A 15 : 1.2412 A 22 <---> A 16 : 1.0733 A 23 <---> A 17 : 0.9730 A 24 <---> A 18 : 0.4705 A 25 <---> A 19 : 0.3560 A 26 <---> A 20 : 3.1145 A 27 A 28 <---> A 21 : 1.5754 A 29 <---> A 22 : 1.6322 A 30 A 31 <---> A 23 : 1.9973 A 32 <---> A 25 : 1.8324 A 33 <---> A 26 : 0.9310 A 34 <---> A 27 : 0.6808 A 35 <---> A 28 : 0.2674 A 36 <---> A 29 : 0.5995 A 37 <---> A 30 : 0.6992 A 38 <---> A 31 : 0.8620 A 39 <---> A 32 : 0.8421 A 40 <---> A 33 : 0.7208 A 41 <---> A 34 : 0.8681 A 42 <---> A 35 : 0.7781 A 43 <---> A 36 : 0.6211 A 44 <---> A 37 : 0.4657 A 45 <---> A 38 : 0.7475 A 46 <---> A 39 : 0.5170 A 47 <---> A 40 : 0.5058 A 48 <---> A 41 : 0.8897 A 49 <---> A 42 : 0.5835 A 50 <---> A 43 : 0.4347 A 51 <---> A 44 : 0.6192 A 52 <---> A 45 : 0.2150 A 53 <---> A 46 : 0.7474 A 54 <---> A 47 : 1.0213 A 55 <---> A 48 : 0.9208 A 56 <---> A 49 : 0.9392 A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 0.4666 A 66 <---> A 61 : 0.0523 A 67 <---> A 62 : 1.0719 A 68 <---> A 63 : 0.7933 A 69 <---> A 64 : 0.8916 A 70 <---> A 65 : 1.2580 A 71 <---> A 66 : 0.6932 A 72 <---> A 67 : 1.0345 A 73 <---> A 68 : 1.4417 A 74 <---> A 69 : 0.9092 A 75 <---> A 70 : 1.6166 A 76 <---> A 71 : 0.8741 A 77 <---> A 72 : 0.2388 A 78 <---> A 73 : 0.3118 A 79 <---> A 74 : 0.3887 A 80 <---> A 75 : 0.7613 A 81 <---> A 76 : 0.9044 A 82 <---> A 77 : 0.6090 A 83 <---> A 78 : 1.7978 A 84 <---> A 79 : 1.9256 A 85 <---> A 80 : 1.3416 A 86 <---> A 81 : 0.5658 A 87 <---> A 82 : 0.4480 A 88 <---> A 83 : 0.9078 A 89 <---> A 84 : 0.3625 A 90 <---> A 85 : 0.4040 A 91 <---> A 86 : 0.4586 A 92 <---> A 87 : 0.4340 A 93 <---> A 88 : 0.3664 A 94 <---> A 89 : 0.4921 A 95 <---> A 90 : 0.6498 A 96 <---> A 91 : 1.5805 A 97 <---> A 92 : 2.8839 A 98 A 99 A 100 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI INFO:: backup file coot-backup/_home_emsley_data_greg-data_1yb5.pdb_Sat_Sep__5_04:46:54_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% ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... WARNING:: Error reading /home/emsley/data/greg-data/1pyd.pdb 0 /home/emsley/data/greg-data/tutorial-modern.pdb 1 /home/emsley/data/greg-data/ins-code-fragment-pre.pdb 2 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 3 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 4 /home/emsley/data/greg-data/tutorial-modern.pdb 5 mainchain 6 /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb 7 regression-test-terminal-residue.pdb 8 atom selection from regression-test-terminal-residue.pdb 9 /home/emsley/data/greg-data/frag-2wot.pdb 10 sphere selection from tutorial-modern.pdb 11 /home/emsley/data/greg-data/tutorial-modern.pdb 13 /home/emsley/data/greg-data/rotamer-test-fragment.pdb 14 /home/emsley/data/greg-data/res098.pdb 15 /home/emsley/data/greg-data/tutorial-modern.pdb 16 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 17 /home/emsley/data/greg-data/pdb3knw.ent 18 /home/emsley/data/greg-data/pdb1py3.ent 21 /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb 22 /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb 23 /home/emsley/data/greg-data/tutorial-modern.pdb 24 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 25 /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb 26 /home/emsley/data/greg-data/tutorial-modern.pdb 27 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 28 /home/emsley/data/greg-data/alt-conf-waters.pdb 29 /home/emsley/data/greg-data/backrub-fragment.pdb 30 Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb 31 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT 32 /home/emsley/data/greg-data/test-TER-OXT.pdb 33 /home/emsley/data/greg-data/val.pdb 34 /home/emsley/data/greg-data/2yie-frag.pdb 35 /home/emsley/data/greg-data/4f8g.pdb 36 /home/emsley/data/greg-data/4f8g.pdb 37 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 38 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 39 /home/emsley/data/greg-data/tutorial-modern.pdb 40 Generic Masked Map 41 difference-map 42 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 43 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 44 averaged-map 45 difference-map 46 /home/emsley/data/greg-data/multi-carbo-coot-2.pdb 47 /home/emsley/data/greg-data/monomer-VAL.pdb 48 /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb 49 atom selection from tutorial-modern.pdb 50 /home/emsley/data/greg-data/monomer-ACT.pdb 51 /home/emsley/data/greg-data/tutorial-modern.pdb 52 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 53 atom selection from tutorial-modern.pdb 54 /home/emsley/data/greg-data/tutorial-modern.pdb 55 /home/emsley/data/greg-data/tutorial-modern.pdb 56 /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb 57 /home/emsley/data/greg-data/tutorial-modern.pdb 58 /home/emsley/data/greg-data/tutorial-modern.pdb 59 /home/emsley/data/greg-data/pdb3hfl.ent 60 /home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT 61 Ideal-A-form-RNA 62 Ideal-A-form-RNA 63 Ideal-A-form-DNA 64 Ideal-A-form-DNA 65 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 66 /home/emsley/data/greg-data/some-waters-with-ter.pdb 67 /home/emsley/data/greg-data/tm+some-waters.pdb 68 /home/emsley/data/greg-data/tutorial-modern.pdb 69 /home/emsley/data/greg-data/water-test-no-cell.pdb 70 /home/emsley/data/greg-data/pathological-water-test.pdb 71 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 72 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 73 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 74 /home/emsley/data/greg-data/tutorial-modern.pdb 75 /home/emsley/data/greg-data/pdb1hvv.ent 76 /home/emsley/data/greg-data/monomer-ACT.pdb 77 /home/emsley/data/greg-data/monomer-NPO.pdb 78 SymOp_-X,-X+Y,-Z+1/3_Copy_of_75 79 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 80 Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb 81 /home/emsley/data/greg-data/tutorial-modern.pdb 82 /home/emsley/data/greg-data/pdb1py3.ent 83 /home/emsley/data/greg-data/tutorial-modern.pdb 84 /home/emsley/data/greg-data/tutorial-modern.pdb 85 /home/emsley/data/greg-data/2goz-manip.pdb 86 rnase_zip_test.pdb.gz 87 /home/emsley/data/greg-data/tutorial-modern.pdb 88 /home/emsley/data/greg-data/HOF.RES 89 /home/emsley/data/greg-data/hollander.ins 92 /home/emsley/data/greg-data/insulin.fcf 93 atom selection from insulin.res 94 atom selection from insulin.res 96 /home/emsley/data/greg-data/horma-p21.res 97 new-horma.ins 98 /home/emsley/data/greg-data/crash.hat 99 /home/emsley/data/greg-data/crash.hat 100 coot-ccp4/monomer-3GP.pdb 101 /home/emsley/data/greg-data/monomer-3GP.pdb 102 /home/emsley/data/greg-data/test-LIG.pdb 103 /home/emsley/data/greg-data/test-LIG.pdb 104 /home/emsley/data/greg-data/monomer-NPO.pdb 105 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 106 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 107 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 108 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 109 Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb 110 /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb 111 /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT 112 /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT 113 Masked (by protein) 114 Fitted ligand #0-0 115 Fitted ligand #0-1 116 Fitted ligand #0-2 117 Fitted ligand #1-0 118 Fitted ligand #1-1 119 Fitted ligand #2-0 120 Fitted ligand #2-1 121 Fitted ligand #2-2 122 Fitted ligand #2-3 123 Fitted ligand #3-0 124 Fitted ligand #3-1 125 Fitted ligand #3-2 126 Fitted ligand #4-0 127 Fitted ligand #5-0 128 Fitted ligand #5-1 129 Fitted ligand #6-0 130 Fitted ligand #6-1 131 Fitted ligand #7-0 132 Fitted ligand #8-0 133 Fitted ligand #8-1 134 Fitted ligand #9-0 135 Fitted ligand #9-1 136 Fitted ligand #9-2 137 coot-ccp4/monomer-3GP.pdb 138 Copy_of_coot-ccp4/monomer-3GP.pdb 139 /home/emsley/data/greg-data/dipole-residues.pdb 140 /home/emsley/data/greg-data/tutorial-modern.pdb 141 /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb 142 /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 143 Ideal-A-form-RNA 144 Copy_of_Ideal-A-form-RNA 145 Copy_of_Ideal-A-form-RNA 146 /home/emsley/data/greg-data/1wly.pdb 147 /home/emsley/data/greg-data/1yb5.pdb ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/2qd9.pdb PDB file /home/emsley/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 148 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LGF.cif INFO:: Reading coordinate file: /home/emsley/data/greg-data/2gtn.pdb PDB file /home/emsley/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 0/337 Molecule 149 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/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LIE.cif INFO:: reference 148 has 169 atoms selected INFO:: moving 149 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_home_emsley_data_greg-data_2gtn.pdb_Sat_Sep__5_04:46:56_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:: making map from mtz filename /home/emsley/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:: 0.0270 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0160 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:: 0.0180 seconds for contour map INFO:: 0.0640 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:: 737280 out of 737280 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0003 st.d: 0.3250 Map statistics: min: -1.4894, max: 2.4019 -1.4407 3 -1.3435 7 -1.2462 16 -1.1489 7 -1.0516 17 -0.9543 61 -0.8570 255 -0.7598 907 -0.6625 3123 -0.5652 9819 -0.4679 26025 -0.3706 54787 -0.2733 87760 -0.1761 106865 -0.0788 105275 0.0185 88484 0.1158 67331 0.2131 50442 0.3103 38437 0.4076 28654 0.5049 21003 0.6022 15144 0.6995 10724 0.7968 7514 0.8940 5100 0.9913 3555 1.0886 2282 1.1859 1498 1.2832 914 1.3804 569 1.4777 316 1.5750 169 1.6723 84 1.7696 44 1.8669 35 1.9641 30 2.0614 9 2.1587 9 2.2560 2 2.3533 4 2.4506 0 INFO:: installing ghost map with name :Map 150 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0004 st.d: 0.3236 Map statistics: min: -1.4496, max: 2.3411 -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 2 2.3885 0 ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... NCS info: [['A', 'B']] ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... 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 155 read successfully no diffs NCS target chain has 93 peers. ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 156 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:59_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:59_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:59_2015_modification_2.pdb.gz %%%%%%%%% 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: 156 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 156 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:59_2015_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:59_2015_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 156 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 156 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:46:59_2015_modification_5.pdb.gz ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1t6q.ent PDB file /home/emsley/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links 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 157 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Sat_Sep__5_04:47:00_2015_modification_0.pdb.gz %%%%%%%%% 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" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 157 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 157 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Sat_Sep__5_04:47:00_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Sat_Sep__5_04:47:00_2015_modification_2.pdb.gz result: [True, True] ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 158 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 158 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:: Matching/moving molecule number 159 to 158 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Sat_Sep__5_04:47:03_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 159 to 158 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_emsley_data_greg-data_pdb1hvv.ent_Sat_Sep__5_04:47:03_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 159 to 158 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_emsley_data_greg-data_pdb1hvv.ent_Sat_Sep__5_04:47:03_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]] 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:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 160 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/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:: 0.0400 seconds to read MTZ file INFO:: 0.0240 seconds to initialize map INFO:: 0.0270 seconds for FFT INFO:: 0.0040 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0100 seconds for contour map INFO:: 0.1050 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 161 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 161 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 161 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 161 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 161 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 161 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 161 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 161 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 161 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 BL DEBUG:: molecule_names ['/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/ins-code-fragment-pre.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/tutorial-modern.pdb', 'mainchain', '/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb', 'regression-test-terminal-residue.pdb', 'atom selection from regression-test-terminal-residue.pdb', '/home/emsley/data/greg-data/frag-2wot.pdb', 'sphere selection from tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rotamer-test-fragment.pdb', '/home/emsley/data/greg-data/res098.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/pdb3knw.ent', '/home/emsley/data/greg-data/pdb1py3.ent', '/home/emsley/data/greg-data/alt-conf-pepflip-test.pdb', '/home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/alt-conf-waters.pdb', '/home/emsley/data/greg-data/backrub-fragment.pdb', 'Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT', '/home/emsley/data/greg-data/test-TER-OXT.pdb', '/home/emsley/data/greg-data/val.pdb', '/home/emsley/data/greg-data/2yie-frag.pdb', '/home/emsley/data/greg-data/4f8g.pdb', '/home/emsley/data/greg-data/4f8g.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/tutorial-modern.pdb', 'Generic Masked Map', 'difference-map', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'averaged-map', 'difference-map', '/home/emsley/data/greg-data/multi-carbo-coot-2.pdb', '/home/emsley/data/greg-data/monomer-VAL.pdb', '/home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb', 'atom selection from tutorial-modern.pdb', '/home/emsley/data/greg-data/monomer-ACT.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', 'atom selection from tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb3hfl.ent', '/home/emsley/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/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/some-waters-with-ter.pdb', '/home/emsley/data/greg-data/tm+some-waters.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/water-test-no-cell.pdb', '/home/emsley/data/greg-data/pathological-water-test.pdb', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb1hvv.ent', '/home/emsley/data/greg-data/monomer-ACT.pdb', '/home/emsley/data/greg-data/monomer-NPO.pdb', 'SymOp_-X,-X+Y,-Z+1/3_Copy_of_75', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb1py3.ent', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/2goz-manip.pdb', 'rnase_zip_test.pdb.gz', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/HOF.RES', '/home/emsley/data/greg-data/hollander.ins', '/home/emsley/data/greg-data/insulin.fcf', 'atom selection from insulin.res', 'atom selection from insulin.res', '/home/emsley/data/greg-data/horma-p21.res', 'new-horma.ins', '/home/emsley/data/greg-data/crash.hat', '/home/emsley/data/greg-data/crash.hat', 'coot-ccp4/monomer-3GP.pdb', '/home/emsley/data/greg-data/monomer-3GP.pdb', '/home/emsley/data/greg-data/test-LIG.pdb', '/home/emsley/data/greg-data/test-LIG.pdb', '/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb', '/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb', '/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT', '/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT', 'Masked (by protein)', 'Fitted ligand #0-0', 'Fitted ligand #0-1', 'Fitted ligand #0-2', 'Fitted ligand #1-0', 'Fitted ligand #1-1', 'Fitted ligand #2-0', 'Fitted ligand #2-1', 'Fitted ligand #2-2', 'Fitted ligand #2-3', 'Fitted ligand #3-0', 'Fitted ligand #3-1', 'Fitted ligand #3-2', 'Fitted ligand #4-0', 'Fitted ligand #5-0', 'Fitted ligand #5-1', 'Fitted ligand #6-0', 'Fitted ligand #6-1', 'Fitted ligand #7-0', 'Fitted ligand #8-0', 'Fitted ligand #8-1', 'Fitted ligand #9-0', 'Fitted ligand #9-1', 'Fitted ligand #9-2', 'coot-ccp4/monomer-3GP.pdb', 'Copy_of_coot-ccp4/monomer-3GP.pdb', '/home/emsley/data/greg-data/dipole-residues.pdb', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb', '/home/emsley/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/emsley/data/greg-data/1wly.pdb', '/home/emsley/data/greg-data/1yb5.pdb', '/home/emsley/data/greg-data/2qd9.pdb', '/home/emsley/data/greg-data/2gtn.pdb', '/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Map 2 NCS average of Chain A type molecules', 'Map 150 NCS average of Chain A type molecules', '/home/emsley/data/greg-data/insulin.res', '/home/emsley/data/greg-data/tutorial-modern.pdb', '/home/emsley/data/greg-data/pdb1t6q.ent', '/home/emsley/data/greg-data/pdb1hvv.ent', '/home/emsley/data/greg-data/pdb1hvv.ent', '/home/emsley/data/greg-data/1hvv_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Map 161 NCS found from matching Chain B onto Chain A', 'Map 161 NCS found from matching Chain C onto Chain A', 'Map 161 NCS found from matching Chain D onto Chain A', 'Map 161 NCS average of Chain A type molecules', 'Map 161 NCS found from matching Chain B onto Chain A', 'Map 161 NCS found from matching Chain C onto Chain A', 'Map 161 NCS found from matching Chain D onto Chain A', 'Map 161 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 ... BL DEBUG:: return scheme is [24.219083786010742, -41.04264831542969, -67.95923614501953] 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/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_alt_conf_rotamers Entering test: test_wiggly_ligands There are 2 data in /home/emsley/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 69.637s 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 (_gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable 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 morning Paul Emsley. Welcome to Coot 0.8.3-pre. 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" _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 69.637s OK Unitest skip does not exist! The following tests were skipped and marked as passed: Libcif horne 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: test_coot_python: coot test passed