testing with python unittest testing with python unittest currently we are here: /lmb/home/pemsley/autobuild/building/lg19.lmb.internal_2017-08-01__T23_30_02/coot-0.8.9-pre /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/bin/coot --no-graphics --script python-tests/coot_unittest.py INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ INFO:: Reading coordinate file: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) INFO:: coot.py imported Running python script /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Morning Paul, Welcome to Coot version 0.8.9-pre (set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.8.9-pre") (use-graphics-interface-state) Running python script /lmb/home/pemsley/.coot-preferences/contact_dots.py name 'coot_menubar_menu' is not defined Running python script /lmb/home/pemsley/.coot-preferences/coot_probe_dots.py Running python script /lmb/home/pemsley/.coot-preferences/pepflip-new.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good morning Paul. Welcome to Coot 0.8.9-pre") (set-display-lists-for-maps 0) load /lmb/home/pemsley/.coot-preferences/angle-factor.scm (set-hardware-stereo-angle-factor 1.50) load /lmb/home/pemsley/.coot-preferences/chain-refine.scm load /lmb/home/pemsley/.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 22.00) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) load /lmb/home/pemsley/.coot-preferences/enhanced-ligand.scm load /lmb/home/pemsley/.coot-preferences/key-bindings.scm (set-add-terminal-residue-do-post-refine 1) (set-terminal-residue-do-rigid-body-refine 0) load /lmb/home/pemsley/.coot-preferences/kill-side-chain.scm load /lmb/home/pemsley/.coot-preferences/morph-march.scm load /lmb/home/pemsley/.coot-preferences/template-key-bindings.scm (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run python-tests/coot_unittest.py Running python script python-tests/coot_unittest.py =============================================================== ==================== Testing ================================== =============================================================== WARNING:: unittest skip not avaliable!!!!!! ==== It seems CCP4_MASTER is setup === ==== CCP4_MASTER: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2 test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... INFO:: Command: (post-go-to-atom-window) ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... INFO:: Command: (close-molecule -2) ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... Molecule number -5 is not a valid model molecule ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2WF6.pdb" 1) WARNING:: Error reading /lmb/home/pemsley/data/greg-data/2WF6.pdb closing molecule number -1 INFO:: Command: (close-molecule -1) ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Command: (info-dialog "Oops, failed to create fragment. No atoms selected Incorrect atom specifier? "//A/100"") INFO:: pre_n_molecules 1 post_n_molecules 1 ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb" 0) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb PDB file /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 1 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (set-go-to-atom-molecule 1) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Wed_Aug__2_00:49:36_2017_modification_0.pdb.gz INFO:: Command: (change-residue-number 1 "A" 68 "" 68 "A") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Wed_Aug__2_00:49:36_2017_modification_1.pdb.gz INFO:: Command: (change-residue-number 1 "A" 69 "" 68 "B") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Wed_Aug__2_00:49:36_2017_modification_2.pdb.gz INFO:: Command: (change-residue-number 1 "A" 67 "" 68 "") pre and post ins codes: A INFO:: Command: (write-pdb-file 1 "post-ins-change.pdb") pass: ['A', 68, '', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'B', ' CA '] pass: ['A', 68, 'A', ' CA '] pass: ['A', 68, '', ' CA '] pass: ['A', 66, '', ' CA '] ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... WARNING:: Error reading bogus.map Read map bogus.map failed ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... WARNING:: Can't find file bogus.mtz INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.075 seconds to read MTZ file INFO:: 0.051 seconds to initialize map INFO:: 0.041 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.014 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.299 seconds for contour map INFO:: 0.48 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: /lmb/home/pemsley/data/greg-data/broken.mtz INFO:: not an mtz file: /lmb/home/pemsley/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 /lmb/home/pemsley/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:: 0.001 seconds to initialize map INFO:: 0.028 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.011 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.239 seconds for contour map INFO:: 0.305 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: Command: (another-level-from-map-molecule-number 2) ok test09_1 (__main__.PdbMtzTestFunctions) db-main makes mainchain ... INFO:: Command: (handle-read-draw-molecule-with-recentre "." 1) WARNING:: Error reading . . is a directory. INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-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: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb INFO:: 8375 fragments found in total of which 0 were 5 peptides target fragment start res: 10 had 29 db fragment hits, ilength=6 target fragment start res: 13 had 1772 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 16 merge fragments 10 to 20 with 2 fit sets to merge The merging is complete mainchain_fragment from 10 to 20 done mainchain_fragment successfully set cell and symmetry INFO:: Command: (db-mainchain 4 "A" 10 20 "forward") ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... INFO:: Command: (set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.50) ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /lmb/home/pemsley/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 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 1000 random trials --- in best_fit_phi_psi() with offset -1 INFO:: Fitting terminal residue without individual rigid body fitting. --- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000 called fit_terminal_residue_generic() residue-seqnum: 1 offset: -1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Aug__2_00:49:40_2017_modification_0.pdb.gz INFO:: Command: (add-terminal-residue 6 "A" 1 1) INFO:: Command: (write-pdb-file 6 "regression-test-terminal-residue.pdb") INFO:: Command: (handle-read-draw-molecule-with-recentre "regression-test-terminal-residue.pdb" 1) INFO:: Reading coordinate file: regression-test-terminal-residue.pdb PDB file regression-test-terminal-residue.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 83/91 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 7 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/atom_selection_from_regression-test-terminal-residue.pdb_Wed_Aug__2_00:49:40_2017_modification_0.pdb.gz INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/frag-2wot.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/frag-2wot.pdb PDB file /lmb/home/pemsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 9 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... INFO:: Command: (n-chains 10) INFO:: Command: (chain_id 10 0) Sphere mol: there are 4 residues in chain B INFO:: Command: (resname-from-serial-number 10 "B" 0) INFO:: Command: (seqnum-from-serial-number 10 "B" 0) INFO:: Command: (insertion-code-from-serial-number 10 "B" 0) INFO:: Command: (resname-from-serial-number 10 "B" 1) INFO:: Command: (seqnum-from-serial-number 10 "B" 1) INFO:: Command: (insertion-code-from-serial-number 10 "B" 1) INFO:: Command: (resname-from-serial-number 10 "B" 2) INFO:: Command: (seqnum-from-serial-number 10 "B" 2) INFO:: Command: (insertion-code-from-serial-number 10 "B" 2) INFO:: Command: (resname-from-serial-number 10 "B" 3) INFO:: Command: (seqnum-from-serial-number 10 "B" 3) INFO:: Command: (insertion-code-from-serial-number 10 "B" 3) Found 20 sphere atoms ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... INFO:: Command: (go-to-view-number 0 1) ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:49:42_2017_modification_0.pdb.gz INFO:: Command: (delete-residue 11 "A" 42 "") residue info (should be False): False ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (set-rotation-centre 31.46 21.41 14.82) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:49:42_2017_modification_0.pdb.gz INFO:: Command: (delete-residue 12 "B" 10 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:49:42_2017_modification_1.pdb.gz INFO:: Command: (delete-residue 12 "B" 11 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:49:42_2017_modification_2.pdb.gz INFO:: Command: (delete-residue 12 "B" 12 "") ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb PDB file /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 13 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] ok test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/res098.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/res098.pdb PDB file /lmb/home/pemsley/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links Molecule 14 read successfully DEBUG:: there were 0 types with no dictionary For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 created 6 bond restraints created 6 angle restraints created 0 plane restraints created 1 chiral vol restraints created 13 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 9 non-bonded restraints initial distortion_score: 26.6475 Initial RMS Z values bonds: 0.22918 angles: 0.43392 torsions: N/A planes: 0.322152 non-bonded: 0 chiral vol: 0.162676 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 141) at 9.94491 Final Estimated RMS Z Scores: bonds: 0.0954112 angles: 0.665415 torsions: N/A planes: 0.648876 non-bonded: 0 chiral vol: 0.590025 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.033 debug:: restraints results 1 5 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_res098.pdb_Wed_Aug__2_00:49:44_2017_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. For atom CE A returning occ 0.7 For atom CE B returning occ 0.2 For atom NZ A returning occ 0.7 For atom NZ B returning occ 0.2 ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 15 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.001 seconds to initialize map INFO:: 0.027 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.011 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.269 seconds for contour map INFO:: 0.334 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:49:45_2017_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:49:45_2017_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 12.0528 INFO:: Command: (auto-fit-best-rotamer 93 "A" "" "A" 15 16 1 0.01) ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb3knw.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3knw.ent PDB file /lmb/home/pemsley/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links 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:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3knw.ent_Wed_Aug__2_00:49:46_2017_modification_0.pdb.gz se_1: [['SE ', ''], [0.7, 2.0, 'SE', ''], [58.8, 66.533, 0.047]] se_2: [['SE ', ''], [0.7, 2.0, 'SE', ''], [60.13112002923666, 69.34847968524429, -0.673518803101735]] ok test16_3 (__main__.PdbMtzTestFunctions) Hs are correctly swapped on a TYR ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 18 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1py3.ent_Wed_Aug__2_00:49:46_2017_modification_0.pdb.gz INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP INFO:: 25 residues had their atoms swapped BL DEBUG:: results: [True, True, True, True] ok test16_4 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 19 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.032 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.013 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.328 seconds for contour map INFO:: 0.404 seconds in total INFO:: Command: (zero-occupancy-residue-range 19 "A" 37 37) here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:49:48_2017_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 INFO:: Command: (close-molecule 19) INFO:: Command: (close-molecule 20) ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb PDB file /lmb/home/pemsley/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 Molecule 21 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-pepflip-test.pdb_Wed_Aug__2_00:49:49_2017_modification_0.pdb.gz flipped 65 A ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /lmb/home/pemsley/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 INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (go-to-view-number 1 1) in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x3946880 omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_modification_0.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_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/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_modification_2.pdb.gz INFO:: Command: (mutate 22 "A" 11 "" "GLY") created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 4 angle links 2 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 27 non-bonded restraints initial distortion_score: 4091.97 Initial RMS Z values bonds: 15.4585 angles: 7.12423 torsions: N/A planes: 2.18109 non-bonded: 126.244 chiral vol: 3.04463 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 118) at -4925.75 Final Estimated RMS Z Scores: bonds: 0.933786 angles: 0.807678 torsions: N/A planes: 2.58973 non-bonded: 0.181009 chiral vol: 0.374877 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 14.972 Refinement elapsed time: 0.015 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_modification_4.pdb.gz INFO:: Command: (mutate 22 "A" 11 "" "LEU") ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.73281 INFO:: Command: (auto-fit-best-rotamer 11 "" "" "A" 22 2 1 1.00) ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 4 angle links 2 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 63 non-bonded restraints initial distortion_score: -6099.8 Initial RMS Z values bonds: 0.904877 angles: 1.49461 torsions: N/A planes: 3.14541 non-bonded: 0.482928 chiral vol: 0.446824 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -6206.77 Final Estimated RMS Z Scores: bonds: 0.910903 angles: 0.733065 torsions: N/A planes: 2.6599 non-bonded: 0.0848076 chiral vol: 0.208863 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 15.112 Refinement elapsed time: 0.012 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Command: (write-pdb-file 22 "tmp-fixed-cis.pdb") ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 23 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.031 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.031 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.013 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.321 seconds for contour map INFO:: 0.397 seconds in total created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 6 non-bonded restraints initial distortion_score: -2794.63 Initial RMS Z values bonds: 1.67379 angles: 1.06965 torsions: N/A planes: 0.611295 non-bonded: 9.24559 chiral vol: 1.46202 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 72) at -2931.62 Final Estimated RMS Z Scores: bonds: 1.12653 angles: 1.40458 torsions: N/A planes: 0.421965 non-bonded: 3.29028 chiral vol: 0.792588 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 16.504 Refinement elapsed time: 0.007 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:49:52_2017_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. refined moved: d= 0.295132018165 ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /lmb/home/pemsley/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 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/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Aug__2_00:49:54_2017_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 INFO:: Command: (set-go-to-atom-molecule 25) imol: 25 residues: [['A', 93, ''], ['A', 92, ''], ['A', 3, ''], ['A', 5, '']] INFO:: created 81 restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints Link restraints: 2 bond links 6 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 5 bond links 15 angle links 10 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 1979 non-bonded restraints initial distortion_score: -21111 Initial RMS Z values bonds: 1.74258 angles: 1.26763 torsions: N/A planes: 0.838264 non-bonded: 0.000533565 chiral vol: 0.894378 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 73) at -21507.2 Final Estimated RMS Z Scores: bonds: 1.14532 angles: 0.684659 torsions: N/A planes: 0.544685 non-bonded: 1.50627e-05 chiral vol: 0.208775 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 18.936 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Aug__2_00:49:54_2017_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. imol: 25 residues: [['A', 41, ''], ['A', 42, ''], ['A', 40, ''], ['A', 39, ''], ['A', 43, '']] INFO:: created 84 restraints created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints Link restraints: 4 bond links 12 angle links 8 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 1393 non-bonded restraints initial distortion_score: -7984.72 Initial RMS Z values bonds: 0.980695 angles: 1.01754 torsions: N/A planes: 1.78749 non-bonded: 4.74047 chiral vol: 10.2816 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 125) at -15999.1 Final Estimated RMS Z Scores: bonds: 1.95686 angles: 1.73857 torsions: N/A planes: 1.66012 non-bonded: 0.0447882 chiral vol: 2.09649 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 20.383 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Aug__2_00:49:54_2017_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. ======= got bond length 1.28808209252 ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 26 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.001 seconds to initialize map INFO:: 0.026 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.011 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.278 seconds for contour map INFO:: 0.342 seconds in total created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -6107.02 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 1.98457 non-bonded: 11.389 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 14) at -11756.1 Final Estimated RMS Z Scores: bonds: 1.8405 angles: 1.7681 torsions: N/A planes: 2.01149 non-bonded: 0.0826445 chiral vol: 1.99953 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 22.032 Refinement elapsed time: 0.042 refinement results: ['', 0, [['Bonds', 'Bonds: 1.840', 1.8404970169067383], ['Angles', 'Angles: 1.768', 1.7681007385253906], ['Planes', 'Planes: 2.011', 2.0114858150482178], ['Non-bonded', 'Non-bonded: 0.287', 0.28747954964637756], ['Chirals', 'Chirals: 2.000', 1.9995266199111938]]] :::: ow factor 1.9049025476 INFO:: setting refinement weight to 16.5350580955 from 60.0 / ( 1.9049025476 * 1.9049025476 ) created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 1793.68 Initial RMS Z values bonds: 0.935808 angles: 1.05798 torsions: N/A planes: 1.98457 non-bonded: 11.389 chiral vol: 11.4845 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 140) at -3158.93 Final Estimated RMS Z Scores: bonds: 0.697622 angles: 0.866569 torsions: N/A planes: 1.68709 non-bonded: 0.00606403 chiral vol: 0.806408 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 22.09 Refinement elapsed time: 0.057 refinement results: ['', 0, [['Bonds', 'Bonds: 0.698', 0.6976221203804016], ['Angles', 'Angles: 0.867', 0.8665685057640076], ['Planes', 'Planes: 1.687', 1.6870890855789185], ['Non-bonded', 'Non-bonded: 0.078', 0.0778719112277031], ['Chirals', 'Chirals: 0.806', 0.8064076900482178]]] :::: ow factor 1.01442185044 ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb PDB file /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 28 read successfully DEBUG:: there were 0 types with no dictionary masking....masking done INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-waters.pdb_Wed_Aug__2_00:49:59_2017_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... INFO:: Command: (update-go-to-atom-window-on-other-molecule-chosen) INFO:: Command: (set-go-to-atom-molecule 0) INFO:: Command: (set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B") ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb" 0) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb PDB file /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 29 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (copy-molecule 29) INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Wed_Aug__2_00:50:00_2017_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Wed_Aug__2_00:50:00_2017_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "/RNASE3GMP/COMPLEX/FWT" "/RNASE3GMP/COMPLEX/PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.036 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.033 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.013 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.264 seconds for contour map INFO:: 0.347 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb PDB file /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 32 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_test-TER-OXT.pdb_Wed_Aug__2_00:50:02_2017_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45 INFO:: Command: (add-OXT-to-residue 32 14 "" "A") WARNING:: This residue already has an OXT - aborting INFO:: Command: (add-OXT-to-residue 32 14 "" "A") INFO:: Command: (write-pdb-file 32 "test-TER-OXT-added.pdb") found TER TER 25 ASP A 14 ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/val.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/val.pdb PDB file /lmb/home/pemsley/data/greg-data/val.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 33 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_val.pdb_Wed_Aug__2_00:50:04_2017_modification_0.pdb.gz INFO:: Command: (mutate 33 "C" 3 "" "HIS") INFO:: Command: (write-pdb-file 33 "his.pdb") ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2yie-frag.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2yie-frag.pdb PDB file /lmb/home/pemsley/data/greg-data/2yie-frag.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 34 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2yie-frag.pdb_Wed_Aug__2_00:50:05_2017_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0404315 rms devi: 0.0471732 max devi: 0.0832785 min devi: 0.0130055 INFO:: Command: (mutate-base 34 "X" 54 "" "C") INFO:: Command: (write-pdb-file 34 "2yie-mutated.pdb") ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/4f8g.pdb PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Molecule 35 read successfully DEBUG:: there were 1 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Wed_Aug__2_00:50:07_2017_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0434566 rms devi: 0.0477873 max devi: 0.073989 min devi: 0.0147744 INFO:: Command: (mutate-base 35 "A" 19 "" "DC") INFO:: Command: (write-pdb-file 35 "test-1.pdb") ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/4f8g.pdb PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Molecule 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Wed_Aug__2_00:50:08_2017_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.0394451 rms devi: 0.0444615 max devi: 0.0694865 min devi: 0.0151341 INFO:: Command: (mutate-base 36 "A" 10 "" "DT") INFO:: Command: (write-pdb-file 36 "test-2.pdb") ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... failed to delete residue atoms A 88 :A: INFO:: Command: (delete-residue-with-full_spec 0 1 "A" 88 "" "A") ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.028 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.027 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.011 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.25 seconds for contour map INFO:: 0.317 seconds in total INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.026 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.012 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.255 seconds for contour map INFO:: 0.32 seconds in total INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 0) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 INFO:: Map statistics: mean: -0.00140896 st.d: 0.305562 INFO:: Map statistics: min: -0.921659 max: 3.05176 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 80118 -0.176642 105928 -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 INFO:: Command: (atom_info_string 39 A 20 CA ) INFO:: Command: (atom_info_string 39 A 21 CA ) INFO:: Command: (atom_info_string 39 A 22 CA ) INFO:: Command: (atom_info_string 39 A 23 CA ) INFO:: Command: (atom_info_string 39 A 24 CA ) INFO:: Command: (atom_info_string 39 A 25 CA ) INFO:: Command: (atom_info_string 39 A 26 CA ) INFO:: Command: (atom_info_string 39 A 27 CA ) INFO:: Command: (atom_info_string 39 A 28 CA ) INFO:: Command: (atom_info_string 39 A 29 CA ) INFO:: Command: (atom_info_string 39 A 30 CA ) INFO:: Command: (atom_info_string 39 A 1 CA ) INFO:: Command: (atom_info_string 39 A 2 CA ) INFO:: Command: (atom_info_string 39 A 3 CA ) INFO:: Command: (atom_info_string 39 A 4 CA ) INFO:: Command: (atom_info_string 39 A 5 CA ) INFO:: Command: (atom_info_string 39 A 6 CA ) INFO:: Command: (atom_info_string 39 A 7 CA ) INFO:: Command: (atom_info_string 39 A 8 CA ) INFO:: Command: (atom_info_string 39 A 9 CA ) INFO:: Command: (atom_info_string 39 A 10 CA ) high-values: [0.8227399587631226, 1.0119965076446533, 1.0171315670013428, 1.068248987197876, 0.7381036281585693, 0.801753580570221, 0.6875786781311035, 0.6362037658691406, 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] INFO:: Map statistics: mean: -0.00140896 st.d: 0.0605043 INFO:: Map statistics: min: -2.99276 max: 0.774316 Map statistics: mean: -0.00140896 st.d: 0.0605043 Map statistics: min: -2.99276, max: 0.774316 -2.94567 2 -2.85149 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 -1.62719 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 0.0679895 2120 0.162166 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, -0.6932032108306885, -0.848896324634552, -0.8271133899688721, -1.0860068798065186, -1.2907466888427734, -1.1838661432266235, -0.947303831577301, -0.893179178237915] ok test29_1 (__main__.PdbMtzTestFunctions) Skeletonize a map ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 42 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.027 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.011 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.273 seconds for contour map INFO:: 0.337 seconds in total INFO:: Command: (close-molecule 42) INFO:: Command: (close-molecule 43) ok test29_2 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.001 seconds to initialize map INFO:: 0.027 seconds for FFT INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.921659 max: 3.05176 INFO:: 0.011 seconds for statistics Map mean: ........ 1.22049e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.275 seconds for contour map INFO:: 0.34 seconds in total INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.027 seconds to read MTZ file INFO:: 0.039 seconds to initialize map INFO:: 0.036 seconds for FFT INFO:: Map statistics: mean: 1.13088e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.877519 max: 3.07133 INFO:: 0.016 seconds for statistics Map mean: ........ 1.13088e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.391 seconds for contour map INFO:: 0.509 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 INFO:: Map statistics: mean: -3.34696e-06 st.d: 0.311048 INFO:: Map statistics: min: -0.916532 max: 3.05151 Map statistics: mean: -3.34696e-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 0.0258784 127242 0.125079 79379 0.224281 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 2.50591 5 2.60511 4 2.70431 2 2.80351 4 2.90271 1 3.00191 2 3.10111 0 INFO:: Map statistics: mean: 3.34818e-06 st.d: 0.00108591 INFO:: Map statistics: min: -0.0109202 max: 0.00950789 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 1167 -0.00351499 2161 -0.00300429 4144 -0.00249359 8444 -0.00198289 16358 -0.00147219 32960 -0.000961487 73381 -0.000450785 158320 5.99161e-05 204515 0.000570618 125580 0.00108132 51959 0.00159202 23884 0.00210272 12694 0.00261342 7552 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:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/multi-carbo-coot-3.pdb" 1) WARNING:: Error reading /lmb/home/pemsley/data/greg-data/multi-carbo-coot-3.pdb ok test30_1 (__main__.PdbMtzTestFunctions) Refine an NAG-ASN Link ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb PDB file /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 3 links INFO:: NCS chain comparison 4/110 Molecule 48 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.009 seconds to initialize map INFO:: 0.013 seconds for FFT INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.875045 max: 2.97757 INFO:: 0.004 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.081 seconds for contour map INFO:: 0.134 seconds in total INFO:: dictionary does not already have NAG dynamic add it now ......... checking for /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab ..that failed - trying /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/NAG-decorations.tab INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_0.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_1.pdb.gz INFO:: link torsion generated from link bond restraint ERROR:: null link 0 in ref INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_2.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 1039 non-bonded restraints initial distortion_score: 30660.5 Initial RMS Z values bonds: 0.360748 angles: 0.606408 torsions: N/A planes: 0.68341 non-bonded: 30.3363 chiral vol: 0.444926 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 82) at -905.506 Final Estimated RMS Z Scores: bonds: 2.3209 angles: 1.94418 torsions: N/A planes: 1.13491 non-bonded: 0.0629911 chiral vol: 1.16184 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 45.197 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: link torsion generated from link bond restraint ERROR:: null link 0 in ref INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 894 non-bonded restraints initial distortion_score: -159.726 Initial RMS Z values bonds: 2.3209 angles: 1.94418 torsions: N/A planes: 1.13491 non-bonded: 0.982695 chiral vol: 1.16184 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 136) at -1073.99 Final Estimated RMS Z Scores: bonds: 2.27428 angles: 1.71843 torsions: N/A planes: 0.816347 non-bonded: 0.0708186 chiral vol: 1.14152 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 45.866 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_5.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 805 non-bonded restraints initial distortion_score: 527.093 Initial RMS Z values bonds: 2.27428 angles: 1.71843 torsions: N/A planes: 0.816347 non-bonded: 2.06757 chiral vol: 1.14152 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 48) at -945.462 Final Estimated RMS Z Scores: bonds: 2.30866 angles: 1.92882 torsions: N/A planes: 1.13624 non-bonded: 0.0791371 chiral vol: 1.12258 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 45.968 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_6.pdb.gz INFO:: replace_coords: 22 atoms updated. ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-VAL.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 50 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 1 CB created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.99701 Initial RMS Z values bonds: 0.542493 angles: 0.164062 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.451586 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.248183 Final Estimated RMS Z Scores: bonds: 0.0122184 angles: 0.0948581 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.145399 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 49.236 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 50 INFO:: Command: (set-undo-molecule 50) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_0.pdb.gz PDB file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 INFO:: Command: (apply-undo) created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.99701 Initial RMS Z values bonds: 0.542493 angles: 0.164062 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.451586 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at 0.248183 Final Estimated RMS Z Scores: bonds: 0.0122184 angles: 0.0948581 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.145399 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 49.293 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. ok test32_0 (__main__.PdbMtzTestFunctions) Test for mangling of hydrogen names from a PDB v 3.0 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 51 read successfully DEBUG:: there were 0 types with no dictionary created 17 bond restraints created 31 angle restraints created 0 plane restraints created 1 chiral vol restraints created 49 restraints INFO:: make_restraints(): made 67 non-bonded restraints initial distortion_score: 903.063 Initial RMS Z values bonds: 5.62114 angles: 3.43297 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.753357 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 165) at 0.474695 Final Estimated RMS Z Scores: bonds: 0.00942912 angles: 0.121017 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.138512 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 52.695 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Wed_Aug__2_00:50:28_2017_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... looping over restraint plane restraint: [plane-restraint: plan {12 atoms} : CB 0.02: : CG 0.02: : CD1 0.02: : CE1 0.02: : CZ 0.02: : CE2 0.02: : CD2 0.02: : OH 0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ] INFO:: Command: (update-go-to-atom-window-on-new-mol) created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 28 restraints INFO:: make_restraints(): made 39 non-bonded restraints initial distortion_score: 2026.18 Initial RMS Z values bonds: 1.1515 angles: 0.847578 torsions: N/A planes: 3.05577 non-bonded: 81.9061 chiral vol: 0.757848 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 62) at -1103.08 Final Estimated RMS Z Scores: bonds: 0.831304 angles: 0.595276 torsions: N/A planes: 0.510595 non-bonded: 0.0856199 chiral vol: 0.26391 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 52.746 Refinement elapsed time: 0.015 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:50:29_2017_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. Bond-length: 2.6034531676 pass intermediate 2.8 tolerance test looping over restraint plane restraint: [plane-restraint: plan {12 atoms} : CB 0.02: : CG 0.02: : CD1 0.02: : CE1 0.02: : CZ 0.02: : CE2 0.02: : CD2 0.02: : OH 0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ] created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: make_restraints(): made 36 non-bonded restraints initial distortion_score: 1354.88 Initial RMS Z values bonds: 14.3437 angles: 0.595276 torsions: N/A planes: 0.510595 non-bonded: 0 chiral vol: 0.26391 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 52) at -1200.38 Final Estimated RMS Z Scores: bonds: 0.295138 angles: 0.273537 torsions: N/A planes: 0.782205 non-bonded: 0 chiral vol: 0.152028 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 52.787 Refinement elapsed time: 0.022 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:50:29_2017_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. OK plane atom CB Bond-length: 1.51797614189 ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... INFO:: wrote mmCIF "coot-test-ala.cif" ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 53 read successfully DEBUG:: there were 1 types with no dictionary ::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_ACT.cif -999999 0 Welcome to Coot looping over restraint plane restraint: [plane-restraint: plan-1 {4 atoms} : C 0.02: : O 0.02: : OXT 0.02: : CH3 0.02: ] created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 15 restraints INFO:: make_restraints(): made 7 non-bonded restraints initial distortion_score: 4848.68 Initial RMS Z values bonds: 0.0119892 angles: 0.00653967 torsions: N/A planes: 0 non-bonded: 689.927 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -295.197 Final Estimated RMS Z Scores: bonds: 0.0561422 angles: 0.371911 torsions: N/A planes: 0.0717946 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 56.288 Refinement elapsed time: 0.017 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-ACT.pdb_Wed_Aug__2_00:50:32_2017_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_2.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_3.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_4.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_6.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_7.pdb.gz INFO:: Command: (n-chains 54) INFO:: Command: (chain_id 54 0) INFO:: Command: (chain_id 54 1) INFO:: Command: (chain_id 54 2) INFO:: Command: (chain_id 54 3) INFO:: Command: (chain_id 54 4) INFO:: Command: (chain_id 54 5) INFO:: Command: (chain_id 54 6) INFO:: Command: (chain_id 54 7) INFO:: Command: (chain_id 54 8) ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... INFO:: Command: (copy-molecule 0) INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Command: (replace-fragement 55 56 "//A70-80") distances: [20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966] ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... found 6 neighbours [['A', 39, ''], ['A', 41, ''], ['A', 38, ''], ['B', 61, ''], ['A', 42, ''], ['B', 60, '']] found 0 neighbours [] ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:41_2017_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: Command: (turn-off-backup 58) INFO:: Command: (rotamer-score 58 "A" 28 "") Rotamer 0 : m-85 100.0 INFO:: Command: (rotamer-score 58 "A" 28 "") Rotamer 1 : t80 90.1668395996 INFO:: Command: (rotamer-score 58 "A" 28 "") Rotamer 2 : p90 50.7077865601 INFO:: Command: (rotamer-score 58 "A" 28 "") Rotamer 3 : m -30 21.4231548309 INFO:: Command: (rotamer-score 58 "A" 28 "") Rotamer 4 : m -30 21.4231548309 INFO:: Command: (turn-on-backup 58) ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /lmb/home/pemsley/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 INFO:: NCS chain comparison 50/87 Molecule 59 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 59 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 > /lmb/home/pemsley/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/_lmb_home_pemsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Wed_Aug__2_00:50:50_2017_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: 8 "A" 1 ""] -> ASP [spec: 8 "A" 2 ""] -> VAL [spec: 8 "A" 3 ""] -> SER [spec: 8 "A" 11 ""] -> LEU [spec: 8 "A" 12 ""] -> PRO [spec: 8 "A" 13 ""] -> PRO [spec: 444383608 "A" 62 ""] -> PRO [spec: 444383608 "A" 63 ""] -> GLY Deletions: [spec: 444383608 "A" 24 ""] [spec: 444383608 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions INFO:: Command: (write-pdb-file 59 "mutated.pdb") ::::: [59, 'A', 1, ''] False False ::::: [59, 'A', 4, ''] True True ::::: [59, 'A', 59, ''] True True ::::: [59, 'A', 60, ''] False False ::::: [59, 'A', 61, ''] False False ::::: [59, 'A', 93, ''] True True ::::: [59, 'A', 94, ''] False False ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 60 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:53_2017_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 60 "A" 10 20 100) INFO:: Command: (seqnum-from-serial-number 60 "A" 90) INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 61 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:57_2017_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 61 "A" 10 20 -100) INFO:: Command: (seqnum-from-serial-number 61 "A" 0) ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb3hfl.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3hfl.ent PDB file /lmb/home/pemsley/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 62 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.024 seconds to read MTZ file INFO:: 0.005 seconds to initialize map INFO:: 0.01 seconds for FFT INFO:: Map statistics: mean: 8.66951e-11 st.d: 0.260405 INFO:: Map statistics: min: -1.03389 max: 1.71787 INFO:: 0.005 seconds for statistics Map mean: ........ 8.66951e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.028 seconds for contour map INFO:: 0.072 seconds in total INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.83405 INFO:: Command: (auto-fit-best-rotamer 52 "" "A" "H" 62 63 0 0.00) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Wed_Aug__2_00:51:01_2017_modification_1.pdb.gz ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269035 rms devi: 0.337196 max devi: 0.547544 min devi: 0.0817551 INFO:: Command: (mutate-base 64 "A" 2 "" "C") mutated base to type C - was A INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269035 rms devi: 0.337196 max devi: 0.547544 min devi: 0.0817551 INFO:: Command: (mutate-base 65 "A" 2 "" "Cr") mutated base to type Cr - was A ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... INFO:: 5 matched atoms had: mean devi: 0.00589883 rms devi: 0.00670957 max devi: 0.0101325 min devi: 0.00258111 INFO:: 5 matched atoms had: mean devi: 0.00725623 rms devi: 0.00778801 max devi: 0.0125644 min devi: 0.00456024 INFO:: 5 matched atoms had: mean devi: 0.271793 rms devi: 0.336384 max devi: 0.533839 min devi: 0.0878288 INFO:: 5 matched atoms had: mean devi: 0.26776 rms devi: 0.326512 max devi: 0.505569 min devi: 0.10459 INFO:: 5 matched atoms had: mean devi: 0.271823 rms devi: 0.336416 max devi: 0.53388 min devi: 0.0879009 INFO:: 5 matched atoms had: mean devi: 0.267791 rms devi: 0.326544 max devi: 0.505617 min devi: 0.104522 INFO:: 5 matched atoms had: mean devi: 0.00717866 rms devi: 0.00770023 max devi: 0.0124098 min devi: 0.00457508 INFO:: 5 matched atoms had: mean devi: 0.00574436 rms devi: 0.00657052 max devi: 0.0099594 min devi: 0.0024248 INFO:: 5 matched atoms had: mean devi: 0.271762 rms devi: 0.336353 max devi: 0.533797 min devi: 0.0877567 INFO:: 5 matched atoms had: mean devi: 0.267729 rms devi: 0.326479 max devi: 0.505521 min devi: 0.104657 INFO:: 5 matched atoms had: mean devi: 0.00585391 rms devi: 0.00666923 max devi: 0.0100827 min devi: 0.00253528 INFO:: 5 matched atoms had: mean devi: 0.00722485 rms devi: 0.00775255 max devi: 0.0125025 min devi: 0.00456535 INFO:: 5 matched atoms had: mean devi: 0.00580961 rms devi: 0.00662938 max devi: 0.0100332 min devi: 0.00249036 INFO:: 5 matched atoms had: mean devi: 0.00719394 rms devi: 0.00771755 max devi: 0.0124407 min devi: 0.00457156 INFO:: 5 matched atoms had: mean devi: 0.267807 rms devi: 0.326561 max devi: 0.505641 min devi: 0.104488 INFO:: 5 matched atoms had: mean devi: 0.27187 rms devi: 0.336463 max devi: 0.533942 min devi: 0.088009 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270191 rms devi: 0.336363 max devi: 0.538427 min devi: 0.0854029 INFO:: Command: (mutate-base 66 "A" 2 "" "DC") mutated base to type DC INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.271895 rms devi: 0.336278 max devi: 0.534478 min devi: 0.0923473 INFO:: Command: (mutate-base 66 "A" 2 "" "DG") mutated base to type DG INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043292 rms devi: 0.00481764 max devi: 0.00738267 min devi: 0.00186162 INFO:: Command: (mutate-base 66 "A" 2 "" "DA") mutated base to type DA INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.265718 rms devi: 0.326008 max devi: 0.501859 min devi: 0.0926641 INFO:: Command: (mutate-base 66 "A" 2 "" "DT") mutated base to type DT INFO:: 5 matched atoms had: mean devi: 0.00589883 rms devi: 0.00670957 max devi: 0.0101325 min devi: 0.00258111 INFO:: 5 matched atoms had: mean devi: 0.00725623 rms devi: 0.00778801 max devi: 0.0125644 min devi: 0.00456024 INFO:: 5 matched atoms had: mean devi: 0.271793 rms devi: 0.336384 max devi: 0.533839 min devi: 0.0878288 INFO:: 5 matched atoms had: mean devi: 0.26776 rms devi: 0.326512 max devi: 0.505569 min devi: 0.10459 INFO:: 5 matched atoms had: mean devi: 0.271823 rms devi: 0.336416 max devi: 0.53388 min devi: 0.0879009 INFO:: 5 matched atoms had: mean devi: 0.267791 rms devi: 0.326544 max devi: 0.505617 min devi: 0.104522 INFO:: 5 matched atoms had: mean devi: 0.00717866 rms devi: 0.00770023 max devi: 0.0124098 min devi: 0.00457508 INFO:: 5 matched atoms had: mean devi: 0.00574436 rms devi: 0.00657052 max devi: 0.0099594 min devi: 0.0024248 INFO:: 5 matched atoms had: mean devi: 0.271762 rms devi: 0.336353 max devi: 0.533797 min devi: 0.0877567 INFO:: 5 matched atoms had: mean devi: 0.267729 rms devi: 0.326479 max devi: 0.505521 min devi: 0.104657 INFO:: 5 matched atoms had: mean devi: 0.00585391 rms devi: 0.00666923 max devi: 0.0100827 min devi: 0.00253528 INFO:: 5 matched atoms had: mean devi: 0.00722485 rms devi: 0.00775255 max devi: 0.0125025 min devi: 0.00456535 INFO:: 5 matched atoms had: mean devi: 0.00580961 rms devi: 0.00662938 max devi: 0.0100332 min devi: 0.00249036 INFO:: 5 matched atoms had: mean devi: 0.00719394 rms devi: 0.00771755 max devi: 0.0124407 min devi: 0.00457156 INFO:: 5 matched atoms had: mean devi: 0.267807 rms devi: 0.326561 max devi: 0.505641 min devi: 0.104488 INFO:: 5 matched atoms had: mean devi: 0.27187 rms devi: 0.336463 max devi: 0.533942 min devi: 0.088009 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270191 rms devi: 0.336363 max devi: 0.538427 min devi: 0.0854029 INFO:: Command: (mutate-base 67 "A" 2 "" "Cd") mutated base to type Cd INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.271895 rms devi: 0.336278 max devi: 0.534478 min devi: 0.0923473 INFO:: Command: (mutate-base 67 "A" 2 "" "Gd") mutated base to type Gd INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043292 rms devi: 0.00481764 max devi: 0.00738267 min devi: 0.00186162 INFO:: Command: (mutate-base 67 "A" 2 "" "Ad") mutated base to type Ad INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.265718 rms devi: 0.326008 max devi: 0.501859 min devi: 0.0926641 INFO:: Command: (mutate-base 67 "A" 2 "" "Td") mutated base to type Td ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... INFO:: Command: (copy-molecule 0) INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz INFO:: Command: (mutate 68 "A" 32 "" "LYS") ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb PDB file /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 69 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (set-rotation-centre 3.00 4.00 5.00) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_some-waters-with-ter.pdb_Wed_Aug__2_00:51:05_2017_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (write-pdb-file 69 "tmp-with-new-water.pdb") ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tm+some-waters.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb PDB file /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: 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: 2.4 3.2 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 55 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tm+some-waters.pdb_Wed_Aug__2_00:51:09_2017_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Command: (write-pdb-file 70 "auto-waters.pdb") ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 71 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Mg") ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb PDB file /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 72 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_water-test-no-cell.pdb_Wed_Aug__2_00:51:21_2017_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pathological-water-test.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb PDB file /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 73 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pathological-water-test.pdb_Wed_Aug__2_00:51:25_2017_modification_0.pdb.gz INFO:: moved 181 water molecules INFO:: Command: (write-pdb-file 73 "waters-moved-failure.pdb") ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... INFO:: Command: (copy-molecule 0) INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.058 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.024 seconds for FFT INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.875045 max: 2.97757 INFO:: 0.006 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.103 seconds for contour map INFO:: 0.191 seconds in total INFO:: Masking around 58 atoms fitting terminal residue with 1000 random trials --- in best_fit_phi_psi() with offset 1 INFO:: Fitting terminal residue without individual rigid body fitting. --- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000 called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:25_2017_modification_0.pdb.gz INFO:: Command: (add-terminal-residue 74 "A" 93 1) ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... INFO:: Command: (copy-molecule 0) DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 76 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 76 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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:26_2017_modification_0.pdb.gz ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 77 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (turn-off-backup 77) 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain) INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 43.60 8.69 12.91) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 45.60 8.69 12.91) 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 47.60 8.69 12.91) 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 49.60 8.69 12.91) 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 51.60 8.69 12.91) INFO:: Command: (renumber-residue-range 77 "D" 1 5 10) 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 53.60 8.69 12.91) 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 55.60 8.69 12.91) 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 57.60 8.69 12.91) 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 59.60 8.69 12.91) 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 61.60 8.69 12.91) INFO:: Command: (renumber-residue-range 77 "E" 11 15 5) 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 63.60 8.69 12.91) 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 65.60 8.69 12.91) 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 67.60 8.69 12.91) 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 69.60 8.69 12.91) 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 71.60 8.69 12.91) INFO:: Command: (renumber-residue-range 77 "F" 16 20 2) INFO:: Command: (n-chains 77) INFO:: Command: (chain_id 77 0) INFO:: Command: (chain_id 77 1) INFO:: Command: (chain_id 77 2) INFO:: Command: (chain_id 77 3) INFO:: Command: (chain_id 77 4) INFO:: Command: (is-solvent-chain-p 77 "A") INFO:: Command: (is-solvent-chain-p 77 "B") INFO:: Command: (is-solvent-chain-p 77 "D") INFO:: Command: (is-solvent-chain-p 77 "E") INFO:: Command: (is-solvent-chain-p 77 "F") INFO:: Command: (resname-from-serial-number 77 "D" 0) INFO:: Command: (seqnum-from-serial-number 77 "D" 0) INFO:: Command: (insertion-code-from-serial-number 77 "D" 0) INFO:: Command: (resname-from-serial-number 77 "D" 1) INFO:: Command: (seqnum-from-serial-number 77 "D" 1) INFO:: Command: (insertion-code-from-serial-number 77 "D" 1) INFO:: Command: (resname-from-serial-number 77 "D" 2) INFO:: Command: (seqnum-from-serial-number 77 "D" 2) INFO:: Command: (insertion-code-from-serial-number 77 "D" 2) INFO:: Command: (resname-from-serial-number 77 "D" 3) INFO:: Command: (seqnum-from-serial-number 77 "D" 3) INFO:: Command: (insertion-code-from-serial-number 77 "D" 3) INFO:: Command: (resname-from-serial-number 77 "D" 4) INFO:: Command: (seqnum-from-serial-number 77 "D" 4) INFO:: Command: (insertion-code-from-serial-number 77 "D" 4) INFO:: Command: (does-residue-exist-p 77 D 1 ) INFO:: Command: (does-residue-exist-p 77 D 2 ) INFO:: Command: (does-residue-exist-p 77 D 3 ) INFO:: Command: (does-residue-exist-p 77 D 4 ) INFO:: Command: (does-residue-exist-p 77 D 5 ) INFO:: Command: (resname-from-serial-number 77 "E" 0) INFO:: Command: (seqnum-from-serial-number 77 "E" 0) INFO:: Command: (insertion-code-from-serial-number 77 "E" 0) INFO:: Command: (resname-from-serial-number 77 "E" 1) INFO:: Command: (seqnum-from-serial-number 77 "E" 1) INFO:: Command: (insertion-code-from-serial-number 77 "E" 1) INFO:: Command: (resname-from-serial-number 77 "E" 2) INFO:: Command: (seqnum-from-serial-number 77 "E" 2) INFO:: Command: (insertion-code-from-serial-number 77 "E" 2) INFO:: Command: (resname-from-serial-number 77 "E" 3) INFO:: Command: (seqnum-from-serial-number 77 "E" 3) INFO:: Command: (insertion-code-from-serial-number 77 "E" 3) INFO:: Command: (resname-from-serial-number 77 "E" 4) INFO:: Command: (seqnum-from-serial-number 77 "E" 4) INFO:: Command: (insertion-code-from-serial-number 77 "E" 4) INFO:: Command: (does-residue-exist-p 77 E 1 ) INFO:: Command: (does-residue-exist-p 77 E 2 ) INFO:: Command: (does-residue-exist-p 77 E 3 ) INFO:: Command: (does-residue-exist-p 77 E 4 ) INFO:: Command: (does-residue-exist-p 77 E 5 ) INFO:: Command: (resname-from-serial-number 77 "F" 0) INFO:: Command: (seqnum-from-serial-number 77 "F" 0) INFO:: Command: (insertion-code-from-serial-number 77 "F" 0) INFO:: Command: (resname-from-serial-number 77 "F" 1) INFO:: Command: (seqnum-from-serial-number 77 "F" 1) INFO:: Command: (insertion-code-from-serial-number 77 "F" 1) INFO:: Command: (resname-from-serial-number 77 "F" 2) INFO:: Command: (seqnum-from-serial-number 77 "F" 2) INFO:: Command: (insertion-code-from-serial-number 77 "F" 2) INFO:: Command: (resname-from-serial-number 77 "F" 3) INFO:: Command: (seqnum-from-serial-number 77 "F" 3) INFO:: Command: (insertion-code-from-serial-number 77 "F" 3) INFO:: Command: (resname-from-serial-number 77 "F" 4) INFO:: Command: (seqnum-from-serial-number 77 "F" 4) INFO:: Command: (insertion-code-from-serial-number 77 "F" 4) INFO:: Command: (does-residue-exist-p 77 F 1 ) INFO:: Command: (does-residue-exist-p 77 F 2 ) INFO:: Command: (does-residue-exist-p 77 F 3 ) INFO:: Command: (does-residue-exist-p 77 F 4 ) INFO:: Command: (does-residue-exist-p 77 F 5 ) INFO:: Command: (renumber-residue-range 77 "E" 1 5 5) INFO:: Command: (renumber-residue-range 77 "F" 1 5 10) INFO:: Command: (turn-on-backup 77) INFO:: Command: (n-chains 77) INFO:: Command: (chain_id 77 2) INFO:: Command: (seqnum-from-serial-number 77 "D" 0) INFO:: Command: (seqnum-from-serial-number 77 "D" 14) ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 78 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 79 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 80 read successfully DEBUG:: there were 1 types with no dictionary -------- starting chain list ----------- INFO:: Command: (n-chains 78) INFO:: Command: (chain_id 78 0) INFO:: Command: (chain_id 78 1) INFO:: Command: (chain_id 78 2) INFO:: Command: (chain_id 78 3) INFO:: Command: (chain_id 78 4) ['A', 'B', 'C', 'D', ''] -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0 0 0.333333 pre-trans: 0 0 0 INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Command: (n-chains 78) INFO:: Command: (chain_id 78 0) INFO:: Command: (chain_id 78 1) INFO:: Command: (chain_id 78 2) INFO:: Command: (chain_id 78 3) INFO:: Command: (chain_id 78 4) INFO:: Command: (chain_id 78 5) INFO:: Command: (chain_id 78 6) INFO:: Command: (chain_id 78 7) INFO:: Command: (chain_id 78 8) INFO:: Command: (chain_id 78 9) INFO:: Command: (chain_id 78 10) INFO:: Command: (chain_id 78 11) ['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K'] INFO:: Command: (write-pdb-file 78 "sym-merged.pdb") ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... INFO:: Command: (copy-molecule 0) INFO:: Command: (copy-molecule 0) INFO:: Matching/moving molecule number 83 to 82 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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:40_2017_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 84 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links 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 85 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: spacegroup: P 21 21 21 INFO:: spacegroup: C 1 2 1 INFO:: Matching/moving molecule number 84 to 85 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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:48_2017_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 86 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:52_2017_modification_0.pdb.gz INFO:: Command: (set-residue-name 86 "A" 37 "" "FRE") INFO:: Command: (n-chains 86) INFO:: Command: (chain_id 86 0) INFO:: Command: (chain_id 86 1) INFO:: Command: (seqnum-from-serial-number 86 "A" 0) INFO:: Command: (insertion-code-from-serial-number 86 "A" 0) INFO:: Command: (seqnum-from-serial-number 86 "A" 1) INFO:: Command: (insertion-code-from-serial-number 86 "A" 1) INFO:: Command: (seqnum-from-serial-number 86 "A" 2) INFO:: Command: (insertion-code-from-serial-number 86 "A" 2) INFO:: Command: (seqnum-from-serial-number 86 "A" 3) INFO:: Command: (insertion-code-from-serial-number 86 "A" 3) INFO:: Command: (seqnum-from-serial-number 86 "A" 4) INFO:: Command: (insertion-code-from-serial-number 86 "A" 4) INFO:: Command: (seqnum-from-serial-number 86 "A" 5) INFO:: Command: (insertion-code-from-serial-number 86 "A" 5) INFO:: Command: (seqnum-from-serial-number 86 "A" 6) INFO:: Command: (insertion-code-from-serial-number 86 "A" 6) INFO:: Command: (seqnum-from-serial-number 86 "A" 7) INFO:: Command: (insertion-code-from-serial-number 86 "A" 7) INFO:: Command: (seqnum-from-serial-number 86 "A" 8) INFO:: Command: (insertion-code-from-serial-number 86 "A" 8) INFO:: Command: (seqnum-from-serial-number 86 "A" 9) INFO:: Command: (insertion-code-from-serial-number 86 "A" 9) INFO:: Command: (seqnum-from-serial-number 86 "A" 10) INFO:: Command: (insertion-code-from-serial-number 86 "A" 10) INFO:: Command: (seqnum-from-serial-number 86 "A" 11) INFO:: Command: (insertion-code-from-serial-number 86 "A" 11) INFO:: Command: (seqnum-from-serial-number 86 "A" 12) INFO:: Command: (insertion-code-from-serial-number 86 "A" 12) INFO:: Command: (seqnum-from-serial-number 86 "A" 13) INFO:: Command: (insertion-code-from-serial-number 86 "A" 13) INFO:: Command: (seqnum-from-serial-number 86 "A" 14) INFO:: Command: (insertion-code-from-serial-number 86 "A" 14) INFO:: Command: (seqnum-from-serial-number 86 "A" 15) INFO:: Command: (insertion-code-from-serial-number 86 "A" 15) INFO:: Command: (seqnum-from-serial-number 86 "A" 16) INFO:: Command: (insertion-code-from-serial-number 86 "A" 16) INFO:: Command: (seqnum-from-serial-number 86 "A" 17) INFO:: Command: (insertion-code-from-serial-number 86 "A" 17) INFO:: Command: (seqnum-from-serial-number 86 "A" 18) INFO:: Command: (insertion-code-from-serial-number 86 "A" 18) INFO:: Command: (seqnum-from-serial-number 86 "A" 19) INFO:: Command: (insertion-code-from-serial-number 86 "A" 19) INFO:: Command: (seqnum-from-serial-number 86 "A" 20) INFO:: Command: (insertion-code-from-serial-number 86 "A" 20) INFO:: Command: (seqnum-from-serial-number 86 "A" 21) INFO:: Command: (insertion-code-from-serial-number 86 "A" 21) INFO:: Command: (seqnum-from-serial-number 86 "A" 22) INFO:: Command: (insertion-code-from-serial-number 86 "A" 22) INFO:: Command: (seqnum-from-serial-number 86 "A" 23) INFO:: Command: (insertion-code-from-serial-number 86 "A" 23) INFO:: Command: (seqnum-from-serial-number 86 "A" 24) INFO:: Command: (insertion-code-from-serial-number 86 "A" 24) INFO:: Command: (seqnum-from-serial-number 86 "A" 25) INFO:: Command: (insertion-code-from-serial-number 86 "A" 25) INFO:: Command: (seqnum-from-serial-number 86 "A" 26) INFO:: Command: (insertion-code-from-serial-number 86 "A" 26) INFO:: Command: (seqnum-from-serial-number 86 "A" 27) INFO:: Command: (insertion-code-from-serial-number 86 "A" 27) INFO:: Command: (seqnum-from-serial-number 86 "A" 28) INFO:: Command: (insertion-code-from-serial-number 86 "A" 28) INFO:: Command: (seqnum-from-serial-number 86 "A" 29) INFO:: Command: (insertion-code-from-serial-number 86 "A" 29) INFO:: Command: (seqnum-from-serial-number 86 "A" 30) INFO:: Command: (insertion-code-from-serial-number 86 "A" 30) INFO:: Command: (seqnum-from-serial-number 86 "A" 31) INFO:: Command: (insertion-code-from-serial-number 86 "A" 31) INFO:: Command: (seqnum-from-serial-number 86 "A" 32) INFO:: Command: (insertion-code-from-serial-number 86 "A" 32) INFO:: Command: (seqnum-from-serial-number 86 "A" 33) INFO:: Command: (insertion-code-from-serial-number 86 "A" 33) INFO:: Command: (seqnum-from-serial-number 86 "A" 34) INFO:: Command: (insertion-code-from-serial-number 86 "A" 34) INFO:: Command: (seqnum-from-serial-number 86 "A" 35) INFO:: Command: (insertion-code-from-serial-number 86 "A" 35) INFO:: Command: (seqnum-from-serial-number 86 "A" 36) INFO:: Command: (insertion-code-from-serial-number 86 "A" 36) INFO:: Command: (seqnum-from-serial-number 86 "A" 37) INFO:: Command: (insertion-code-from-serial-number 86 "A" 37) INFO:: Command: (seqnum-from-serial-number 86 "A" 38) INFO:: Command: (insertion-code-from-serial-number 86 "A" 38) INFO:: Command: (seqnum-from-serial-number 86 "A" 39) INFO:: Command: (insertion-code-from-serial-number 86 "A" 39) INFO:: Command: (seqnum-from-serial-number 86 "A" 40) INFO:: Command: (insertion-code-from-serial-number 86 "A" 40) INFO:: Command: (seqnum-from-serial-number 86 "A" 41) INFO:: Command: (insertion-code-from-serial-number 86 "A" 41) INFO:: Command: (seqnum-from-serial-number 86 "A" 42) INFO:: Command: (insertion-code-from-serial-number 86 "A" 42) INFO:: Command: (seqnum-from-serial-number 86 "A" 43) INFO:: Command: (insertion-code-from-serial-number 86 "A" 43) INFO:: Command: (seqnum-from-serial-number 86 "A" 44) INFO:: Command: (insertion-code-from-serial-number 86 "A" 44) INFO:: Command: (seqnum-from-serial-number 86 "A" 45) INFO:: Command: (insertion-code-from-serial-number 86 "A" 45) INFO:: Command: (seqnum-from-serial-number 86 "A" 46) INFO:: Command: (insertion-code-from-serial-number 86 "A" 46) INFO:: Command: (seqnum-from-serial-number 86 "A" 47) INFO:: Command: (insertion-code-from-serial-number 86 "A" 47) INFO:: Command: (seqnum-from-serial-number 86 "A" 48) INFO:: Command: (insertion-code-from-serial-number 86 "A" 48) INFO:: Command: (seqnum-from-serial-number 86 "A" 49) INFO:: Command: (insertion-code-from-serial-number 86 "A" 49) INFO:: Command: (seqnum-from-serial-number 86 "A" 50) INFO:: Command: (insertion-code-from-serial-number 86 "A" 50) INFO:: Command: (seqnum-from-serial-number 86 "A" 51) INFO:: Command: (insertion-code-from-serial-number 86 "A" 51) INFO:: Command: (seqnum-from-serial-number 86 "A" 52) INFO:: Command: (insertion-code-from-serial-number 86 "A" 52) INFO:: Command: (seqnum-from-serial-number 86 "A" 53) INFO:: Command: (insertion-code-from-serial-number 86 "A" 53) INFO:: Command: (seqnum-from-serial-number 86 "A" 54) INFO:: Command: (insertion-code-from-serial-number 86 "A" 54) INFO:: Command: (seqnum-from-serial-number 86 "A" 55) INFO:: Command: (insertion-code-from-serial-number 86 "A" 55) INFO:: Command: (seqnum-from-serial-number 86 "A" 56) INFO:: Command: (insertion-code-from-serial-number 86 "A" 56) INFO:: Command: (seqnum-from-serial-number 86 "A" 57) INFO:: Command: (insertion-code-from-serial-number 86 "A" 57) INFO:: Command: (seqnum-from-serial-number 86 "A" 58) INFO:: Command: (insertion-code-from-serial-number 86 "A" 58) INFO:: Command: (seqnum-from-serial-number 86 "A" 59) INFO:: Command: (insertion-code-from-serial-number 86 "A" 59) INFO:: Command: (seqnum-from-serial-number 86 "A" 60) INFO:: Command: (insertion-code-from-serial-number 86 "A" 60) INFO:: Command: (seqnum-from-serial-number 86 "A" 61) INFO:: Command: (insertion-code-from-serial-number 86 "A" 61) INFO:: Command: (seqnum-from-serial-number 86 "A" 62) INFO:: Command: (insertion-code-from-serial-number 86 "A" 62) INFO:: Command: (seqnum-from-serial-number 86 "A" 63) INFO:: Command: (insertion-code-from-serial-number 86 "A" 63) INFO:: Command: (seqnum-from-serial-number 86 "A" 64) INFO:: Command: (insertion-code-from-serial-number 86 "A" 64) INFO:: Command: (seqnum-from-serial-number 86 "A" 65) INFO:: Command: (insertion-code-from-serial-number 86 "A" 65) INFO:: Command: (seqnum-from-serial-number 86 "A" 66) INFO:: Command: (insertion-code-from-serial-number 86 "A" 66) INFO:: Command: (seqnum-from-serial-number 86 "A" 67) INFO:: Command: (insertion-code-from-serial-number 86 "A" 67) INFO:: Command: (seqnum-from-serial-number 86 "A" 68) INFO:: Command: (insertion-code-from-serial-number 86 "A" 68) INFO:: Command: (seqnum-from-serial-number 86 "A" 69) INFO:: Command: (insertion-code-from-serial-number 86 "A" 69) INFO:: Command: (seqnum-from-serial-number 86 "A" 70) INFO:: Command: (insertion-code-from-serial-number 86 "A" 70) INFO:: Command: (seqnum-from-serial-number 86 "A" 71) INFO:: Command: (insertion-code-from-serial-number 86 "A" 71) INFO:: Command: (seqnum-from-serial-number 86 "A" 72) INFO:: Command: (insertion-code-from-serial-number 86 "A" 72) INFO:: Command: (seqnum-from-serial-number 86 "A" 73) INFO:: Command: (insertion-code-from-serial-number 86 "A" 73) INFO:: Command: (seqnum-from-serial-number 86 "A" 74) INFO:: Command: (insertion-code-from-serial-number 86 "A" 74) INFO:: Command: (seqnum-from-serial-number 86 "A" 75) INFO:: Command: (insertion-code-from-serial-number 86 "A" 75) INFO:: Command: (seqnum-from-serial-number 86 "A" 76) INFO:: Command: (insertion-code-from-serial-number 86 "A" 76) INFO:: Command: (seqnum-from-serial-number 86 "A" 77) INFO:: Command: (insertion-code-from-serial-number 86 "A" 77) INFO:: Command: (seqnum-from-serial-number 86 "A" 78) INFO:: Command: (insertion-code-from-serial-number 86 "A" 78) INFO:: Command: (seqnum-from-serial-number 86 "A" 79) INFO:: Command: (insertion-code-from-serial-number 86 "A" 79) INFO:: Command: (seqnum-from-serial-number 86 "A" 80) INFO:: Command: (insertion-code-from-serial-number 86 "A" 80) INFO:: Command: (seqnum-from-serial-number 86 "A" 81) INFO:: Command: (insertion-code-from-serial-number 86 "A" 81) INFO:: Command: (seqnum-from-serial-number 86 "A" 82) INFO:: Command: (insertion-code-from-serial-number 86 "A" 82) INFO:: Command: (seqnum-from-serial-number 86 "A" 83) INFO:: Command: (insertion-code-from-serial-number 86 "A" 83) INFO:: Command: (seqnum-from-serial-number 86 "A" 84) INFO:: Command: (insertion-code-from-serial-number 86 "A" 84) INFO:: Command: (seqnum-from-serial-number 86 "A" 85) INFO:: Command: (insertion-code-from-serial-number 86 "A" 85) INFO:: Command: (seqnum-from-serial-number 86 "A" 86) INFO:: Command: (insertion-code-from-serial-number 86 "A" 86) INFO:: Command: (seqnum-from-serial-number 86 "A" 87) INFO:: Command: (insertion-code-from-serial-number 86 "A" 87) INFO:: Command: (seqnum-from-serial-number 86 "A" 88) INFO:: Command: (insertion-code-from-serial-number 86 "A" 88) INFO:: Command: (seqnum-from-serial-number 86 "A" 89) INFO:: Command: (insertion-code-from-serial-number 86 "A" 89) INFO:: Command: (seqnum-from-serial-number 86 "A" 90) INFO:: Command: (insertion-code-from-serial-number 86 "A" 90) INFO:: Command: (seqnum-from-serial-number 86 "A" 91) INFO:: Command: (insertion-code-from-serial-number 86 "A" 91) INFO:: Command: (seqnum-from-serial-number 86 "A" 92) INFO:: Command: (insertion-code-from-serial-number 86 "A" 92) INFO:: Command: (seqnum-from-serial-number 86 "B" 0) INFO:: Command: (insertion-code-from-serial-number 86 "B" 0) INFO:: Command: (seqnum-from-serial-number 86 "B" 1) INFO:: Command: (insertion-code-from-serial-number 86 "B" 1) INFO:: Command: (seqnum-from-serial-number 86 "B" 2) INFO:: Command: (insertion-code-from-serial-number 86 "B" 2) INFO:: Command: (seqnum-from-serial-number 86 "B" 3) INFO:: Command: (insertion-code-from-serial-number 86 "B" 3) INFO:: Command: (seqnum-from-serial-number 86 "B" 4) INFO:: Command: (insertion-code-from-serial-number 86 "B" 4) INFO:: Command: (seqnum-from-serial-number 86 "B" 5) INFO:: Command: (insertion-code-from-serial-number 86 "B" 5) INFO:: Command: (seqnum-from-serial-number 86 "B" 6) INFO:: Command: (insertion-code-from-serial-number 86 "B" 6) INFO:: Command: (seqnum-from-serial-number 86 "B" 7) INFO:: Command: (insertion-code-from-serial-number 86 "B" 7) INFO:: Command: (seqnum-from-serial-number 86 "B" 8) INFO:: Command: (insertion-code-from-serial-number 86 "B" 8) INFO:: Command: (seqnum-from-serial-number 86 "B" 9) INFO:: Command: (insertion-code-from-serial-number 86 "B" 9) INFO:: Command: (seqnum-from-serial-number 86 "B" 10) INFO:: Command: (insertion-code-from-serial-number 86 "B" 10) INFO:: Command: (seqnum-from-serial-number 86 "B" 11) INFO:: Command: (insertion-code-from-serial-number 86 "B" 11) INFO:: Command: (seqnum-from-serial-number 86 "B" 12) INFO:: Command: (insertion-code-from-serial-number 86 "B" 12) INFO:: Command: (seqnum-from-serial-number 86 "B" 13) INFO:: Command: (insertion-code-from-serial-number 86 "B" 13) INFO:: Command: (seqnum-from-serial-number 86 "B" 14) INFO:: Command: (insertion-code-from-serial-number 86 "B" 14) INFO:: Command: (seqnum-from-serial-number 86 "B" 15) INFO:: Command: (insertion-code-from-serial-number 86 "B" 15) INFO:: Command: (seqnum-from-serial-number 86 "B" 16) INFO:: Command: (insertion-code-from-serial-number 86 "B" 16) INFO:: Command: (seqnum-from-serial-number 86 "B" 17) INFO:: Command: (insertion-code-from-serial-number 86 "B" 17) INFO:: Command: (seqnum-from-serial-number 86 "B" 18) INFO:: Command: (insertion-code-from-serial-number 86 "B" 18) INFO:: Command: (seqnum-from-serial-number 86 "B" 19) INFO:: Command: (insertion-code-from-serial-number 86 "B" 19) INFO:: Command: (seqnum-from-serial-number 86 "B" 20) INFO:: Command: (insertion-code-from-serial-number 86 "B" 20) INFO:: Command: (seqnum-from-serial-number 86 "B" 21) INFO:: Command: (insertion-code-from-serial-number 86 "B" 21) INFO:: Command: (seqnum-from-serial-number 86 "B" 22) INFO:: Command: (insertion-code-from-serial-number 86 "B" 22) INFO:: Command: (seqnum-from-serial-number 86 "B" 23) INFO:: Command: (insertion-code-from-serial-number 86 "B" 23) INFO:: Command: (seqnum-from-serial-number 86 "B" 24) INFO:: Command: (insertion-code-from-serial-number 86 "B" 24) INFO:: Command: (seqnum-from-serial-number 86 "B" 25) INFO:: Command: (insertion-code-from-serial-number 86 "B" 25) INFO:: Command: (seqnum-from-serial-number 86 "B" 26) INFO:: Command: (insertion-code-from-serial-number 86 "B" 26) INFO:: Command: (seqnum-from-serial-number 86 "B" 27) INFO:: Command: (insertion-code-from-serial-number 86 "B" 27) INFO:: Command: (seqnum-from-serial-number 86 "B" 28) INFO:: Command: (insertion-code-from-serial-number 86 "B" 28) INFO:: Command: (seqnum-from-serial-number 86 "B" 29) INFO:: Command: (insertion-code-from-serial-number 86 "B" 29) INFO:: Command: (seqnum-from-serial-number 86 "B" 30) INFO:: Command: (insertion-code-from-serial-number 86 "B" 30) INFO:: Command: (seqnum-from-serial-number 86 "B" 31) INFO:: Command: (insertion-code-from-serial-number 86 "B" 31) INFO:: Command: (seqnum-from-serial-number 86 "B" 32) INFO:: Command: (insertion-code-from-serial-number 86 "B" 32) INFO:: Command: (seqnum-from-serial-number 86 "B" 33) INFO:: Command: (insertion-code-from-serial-number 86 "B" 33) INFO:: Command: (seqnum-from-serial-number 86 "B" 34) INFO:: Command: (insertion-code-from-serial-number 86 "B" 34) INFO:: Command: (seqnum-from-serial-number 86 "B" 35) INFO:: Command: (insertion-code-from-serial-number 86 "B" 35) INFO:: Command: (seqnum-from-serial-number 86 "B" 36) INFO:: Command: (insertion-code-from-serial-number 86 "B" 36) INFO:: Command: (seqnum-from-serial-number 86 "B" 37) INFO:: Command: (insertion-code-from-serial-number 86 "B" 37) INFO:: Command: 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86 "B" 10) INFO:: Command: (insertion-code-from-serial-number 86 "B" 10) INFO:: Command: (seqnum-from-serial-number 86 "B" 11) INFO:: Command: (insertion-code-from-serial-number 86 "B" 11) INFO:: Command: (seqnum-from-serial-number 86 "B" 12) INFO:: Command: (insertion-code-from-serial-number 86 "B" 12) INFO:: Command: (seqnum-from-serial-number 86 "B" 13) INFO:: Command: (insertion-code-from-serial-number 86 "B" 13) INFO:: Command: (seqnum-from-serial-number 86 "B" 14) INFO:: Command: (insertion-code-from-serial-number 86 "B" 14) INFO:: Command: (seqnum-from-serial-number 86 "B" 15) INFO:: Command: (insertion-code-from-serial-number 86 "B" 15) INFO:: Command: (seqnum-from-serial-number 86 "B" 16) INFO:: Command: (insertion-code-from-serial-number 86 "B" 16) INFO:: Command: (seqnum-from-serial-number 86 "B" 17) INFO:: Command: (insertion-code-from-serial-number 86 "B" 17) INFO:: Command: (seqnum-from-serial-number 86 "B" 18) INFO:: Command: (insertion-code-from-serial-number 86 "B" 18) INFO:: Command: (seqnum-from-serial-number 86 "B" 19) INFO:: Command: (insertion-code-from-serial-number 86 "B" 19) INFO:: Command: (seqnum-from-serial-number 86 "B" 20) INFO:: Command: (insertion-code-from-serial-number 86 "B" 20) INFO:: Command: (seqnum-from-serial-number 86 "B" 21) INFO:: Command: (insertion-code-from-serial-number 86 "B" 21) INFO:: Command: (seqnum-from-serial-number 86 "B" 22) INFO:: Command: (insertion-code-from-serial-number 86 "B" 22) INFO:: Command: (seqnum-from-serial-number 86 "B" 23) INFO:: Command: (insertion-code-from-serial-number 86 "B" 23) INFO:: Command: (seqnum-from-serial-number 86 "B" 24) INFO:: Command: (insertion-code-from-serial-number 86 "B" 24) INFO:: Command: (seqnum-from-serial-number 86 "B" 25) INFO:: Command: (insertion-code-from-serial-number 86 "B" 25) INFO:: Command: (seqnum-from-serial-number 86 "B" 26) INFO:: Command: (insertion-code-from-serial-number 86 "B" 26) INFO:: Command: (seqnum-from-serial-number 86 "B" 27) INFO:: Command: (insertion-code-from-serial-number 86 "B" 27) INFO:: Command: (seqnum-from-serial-number 86 "B" 28) INFO:: Command: (insertion-code-from-serial-number 86 "B" 28) INFO:: Command: (seqnum-from-serial-number 86 "B" 29) INFO:: Command: (insertion-code-from-serial-number 86 "B" 29) INFO:: Command: (seqnum-from-serial-number 86 "B" 30) INFO:: Command: (insertion-code-from-serial-number 86 "B" 30) INFO:: Command: (seqnum-from-serial-number 86 "B" 31) INFO:: Command: (insertion-code-from-serial-number 86 "B" 31) INFO:: Command: (seqnum-from-serial-number 86 "B" 32) INFO:: Command: (insertion-code-from-serial-number 86 "B" 32) INFO:: Command: (seqnum-from-serial-number 86 "B" 33) INFO:: Command: (insertion-code-from-serial-number 86 "B" 33) INFO:: Command: (seqnum-from-serial-number 86 "B" 34) INFO:: Command: (insertion-code-from-serial-number 86 "B" 34) INFO:: Command: (seqnum-from-serial-number 86 "B" 35) INFO:: Command: (insertion-code-from-serial-number 86 "B" 35) INFO:: Command: (seqnum-from-serial-number 86 "B" 36) INFO:: Command: (insertion-code-from-serial-number 86 "B" 36) INFO:: Command: (seqnum-from-serial-number 86 "B" 37) INFO:: Command: (insertion-code-from-serial-number 86 "B" 37) INFO:: Command: (seqnum-from-serial-number 86 "B" 38) INFO:: Command: (insertion-code-from-serial-number 86 "B" 38) INFO:: Command: (seqnum-from-serial-number 86 "B" 39) INFO:: Command: (insertion-code-from-serial-number 86 "B" 39) INFO:: Command: (seqnum-from-serial-number 86 "B" 40) INFO:: Command: (insertion-code-from-serial-number 86 "B" 40) INFO:: Command: (seqnum-from-serial-number 86 "B" 41) INFO:: Command: (insertion-code-from-serial-number 86 "B" 41) INFO:: Command: (seqnum-from-serial-number 86 "B" 42) INFO:: Command: (insertion-code-from-serial-number 86 "B" 42) INFO:: Command: (seqnum-from-serial-number 86 "B" 43) INFO:: Command: (insertion-code-from-serial-number 86 "B" 43) INFO:: Command: (seqnum-from-serial-number 86 "B" 44) INFO:: Command: (insertion-code-from-serial-number 86 "B" 44) INFO:: Command: (seqnum-from-serial-number 86 "B" 45) INFO:: Command: (insertion-code-from-serial-number 86 "B" 45) INFO:: Command: (seqnum-from-serial-number 86 "B" 46) INFO:: Command: (insertion-code-from-serial-number 86 "B" 46) INFO:: Command: (seqnum-from-serial-number 86 "B" 47) INFO:: Command: (insertion-code-from-serial-number 86 "B" 47) INFO:: Command: (seqnum-from-serial-number 86 "B" 48) INFO:: Command: (insertion-code-from-serial-number 86 "B" 48) INFO:: Command: (seqnum-from-serial-number 86 "B" 49) INFO:: Command: (insertion-code-from-serial-number 86 "B" 49) INFO:: Command: (seqnum-from-serial-number 86 "B" 50) INFO:: Command: (insertion-code-from-serial-number 86 "B" 50) INFO:: Command: (seqnum-from-serial-number 86 "B" 51) INFO:: Command: (insertion-code-from-serial-number 86 "B" 51) INFO:: Command: (seqnum-from-serial-number 86 "B" 52) INFO:: Command: (insertion-code-from-serial-number 86 "B" 52) INFO:: Command: (seqnum-from-serial-number 86 "B" 53) INFO:: Command: (insertion-code-from-serial-number 86 "B" 53) INFO:: Command: (seqnum-from-serial-number 86 "B" 54) INFO:: Command: (insertion-code-from-serial-number 86 "B" 54) INFO:: Command: (seqnum-from-serial-number 86 "B" 55) INFO:: Command: (insertion-code-from-serial-number 86 "B" 55) INFO:: Command: (seqnum-from-serial-number 86 "B" 56) INFO:: Command: (insertion-code-from-serial-number 86 "B" 56) INFO:: Command: (seqnum-from-serial-number 86 "B" 57) INFO:: Command: (insertion-code-from-serial-number 86 "B" 57) INFO:: Command: (seqnum-from-serial-number 86 "B" 58) INFO:: Command: (insertion-code-from-serial-number 86 "B" 58) INFO:: Command: (seqnum-from-serial-number 86 "B" 59) INFO:: Command: (insertion-code-from-serial-number 86 "B" 59) INFO:: Command: (seqnum-from-serial-number 86 "B" 60) INFO:: Command: (insertion-code-from-serial-number 86 "B" 60) INFO:: Command: (seqnum-from-serial-number 86 "B" 61) INFO:: Command: (insertion-code-from-serial-number 86 "B" 61) INFO:: Command: (seqnum-from-serial-number 86 "B" 62) INFO:: Command: (insertion-code-from-serial-number 86 "B" 62) INFO:: Command: (seqnum-from-serial-number 86 "B" 63) INFO:: Command: (insertion-code-from-serial-number 86 "B" 63) INFO:: Command: (seqnum-from-serial-number 86 "B" 64) INFO:: Command: (insertion-code-from-serial-number 86 "B" 64) INFO:: Command: (seqnum-from-serial-number 86 "B" 65) INFO:: Command: (insertion-code-from-serial-number 86 "B" 65) INFO:: Command: (seqnum-from-serial-number 86 "B" 66) INFO:: Command: (insertion-code-from-serial-number 86 "B" 66) INFO:: Command: (seqnum-from-serial-number 86 "B" 67) INFO:: Command: (insertion-code-from-serial-number 86 "B" 67) INFO:: Command: (seqnum-from-serial-number 86 "B" 68) INFO:: Command: (insertion-code-from-serial-number 86 "B" 68) INFO:: Command: (seqnum-from-serial-number 86 "B" 69) INFO:: Command: (insertion-code-from-serial-number 86 "B" 69) INFO:: Command: (seqnum-from-serial-number 86 "B" 70) INFO:: Command: (insertion-code-from-serial-number 86 "B" 70) INFO:: Command: (seqnum-from-serial-number 86 "B" 71) INFO:: Command: (insertion-code-from-serial-number 86 "B" 71) INFO:: Command: (seqnum-from-serial-number 86 "B" 72) INFO:: Command: (insertion-code-from-serial-number 86 "B" 72) INFO:: Command: (seqnum-from-serial-number 86 "B" 73) INFO:: Command: (insertion-code-from-serial-number 86 "B" 73) INFO:: Command: (seqnum-from-serial-number 86 "B" 74) INFO:: Command: (insertion-code-from-serial-number 86 "B" 74) INFO:: Command: (seqnum-from-serial-number 86 "B" 75) INFO:: Command: (insertion-code-from-serial-number 86 "B" 75) INFO:: Command: (seqnum-from-serial-number 86 "B" 76) INFO:: Command: (insertion-code-from-serial-number 86 "B" 76) INFO:: Command: (seqnum-from-serial-number 86 "B" 77) INFO:: Command: (insertion-code-from-serial-number 86 "B" 77) INFO:: Command: (seqnum-from-serial-number 86 "B" 78) INFO:: Command: (insertion-code-from-serial-number 86 "B" 78) INFO:: Command: (seqnum-from-serial-number 86 "B" 79) INFO:: Command: (insertion-code-from-serial-number 86 "B" 79) INFO:: Command: (seqnum-from-serial-number 86 "B" 80) INFO:: Command: (insertion-code-from-serial-number 86 "B" 80) INFO:: Command: (seqnum-from-serial-number 86 "B" 81) INFO:: Command: (insertion-code-from-serial-number 86 "B" 81) INFO:: Command: (seqnum-from-serial-number 86 "B" 82) INFO:: Command: (insertion-code-from-serial-number 86 "B" 82) INFO:: Command: (seqnum-from-serial-number 86 "B" 83) INFO:: Command: (insertion-code-from-serial-number 86 "B" 83) INFO:: Command: (seqnum-from-serial-number 86 "B" 84) INFO:: Command: (insertion-code-from-serial-number 86 "B" 84) INFO:: Command: (seqnum-from-serial-number 86 "B" 85) INFO:: Command: (insertion-code-from-serial-number 86 "B" 85) INFO:: Command: (seqnum-from-serial-number 86 "B" 86) INFO:: Command: (insertion-code-from-serial-number 86 "B" 86) INFO:: Command: (seqnum-from-serial-number 86 "B" 87) INFO:: Command: (insertion-code-from-serial-number 86 "B" 87) INFO:: Command: (seqnum-from-serial-number 86 "B" 88) INFO:: Command: (insertion-code-from-serial-number 86 "B" 88) INFO:: Command: (seqnum-from-serial-number 86 "B" 89) INFO:: Command: (insertion-code-from-serial-number 86 "B" 89) INFO:: Command: (seqnum-from-serial-number 86 "B" 90) INFO:: Command: (insertion-code-from-serial-number 86 "B" 90) INFO:: Command: (seqnum-from-serial-number 86 "B" 91) INFO:: Command: (insertion-code-from-serial-number 86 "B" 91) INFO:: Command: (seqnum-from-serial-number 86 "B" 92) INFO:: Command: (insertion-code-from-serial-number 86 "B" 92) INFO:: Command: (seqnum-from-serial-number 86 "B" 93) INFO:: Command: (insertion-code-from-serial-number 86 "B" 93) INFO:: Command: (seqnum-from-serial-number 86 "B" 94) INFO:: Command: (insertion-code-from-serial-number 86 "B" 94) INFO:: Command: (seqnum-from-serial-number 86 "B" 95) INFO:: Command: (insertion-code-from-serial-number 86 "B" 95) 0 [86, 'A', 1, ''] 1 [86, 'A', 2, ''] 2 [86, 'A', 3, ''] 3 [86, 'A', 4, ''] 4 [86, 'A', 5, ''] 5 [86, 'A', 6, ''] 6 [86, 'A', 7, ''] 7 [86, 'A', 8, ''] 8 [86, 'A', 9, ''] 9 [86, 'A', 10, ''] 10 [86, 'A', 11, ''] 11 [86, 'A', 12, ''] 12 [86, 'A', 13, ''] 13 [86, 'A', 14, ''] 14 [86, 'A', 15, ''] 15 [86, 'A', 16, ''] 16 [86, 'A', 17, ''] 17 [86, 'A', 18, ''] 18 [86, 'A', 19, ''] 19 [86, 'A', 20, ''] 20 [86, 'A', 21, ''] 21 [86, 'A', 22, ''] 22 [86, 'A', 23, ''] 23 [86, 'A', 24, ''] 24 [86, 'A', 25, ''] 25 [86, 'A', 26, ''] 26 [86, 'A', 27, ''] 27 [86, 'A', 28, ''] 28 [86, 'A', 29, ''] 29 [86, 'A', 30, ''] 30 [86, 'A', 31, ''] 31 [86, 'A', 32, ''] 32 [86, 'A', 33, ''] 33 [86, 'A', 34, ''] 34 [86, 'A', 35, ''] 35 [86, 'A', 36, ''] 36 [86, 'A', 37, ''] 36 [86, 'A', 37, ''] 37 [86, 'A', 38, ''] 38 [86, 'A', 39, ''] 39 [86, 'A', 40, ''] 40 [86, 'A', 41, ''] 41 [86, 'A', 42, ''] 42 [86, 'A', 43, ''] 43 [86, 'A', 44, ''] 44 [86, 'A', 45, ''] 45 [86, 'A', 46, ''] 46 [86, 'A', 47, ''] 47 [86, 'A', 48, ''] 48 [86, 'A', 49, ''] 49 [86, 'A', 50, ''] 50 [86, 'A', 51, ''] 51 [86, 'A', 52, ''] 52 [86, 'A', 53, ''] 53 [86, 'A', 54, ''] 54 [86, 'A', 55, ''] 55 [86, 'A', 56, ''] 56 [86, 'A', 57, ''] 57 [86, 'A', 58, ''] 58 [86, 'A', 59, ''] 59 [86, 'A', 60, ''] 60 [86, 'A', 61, ''] 61 [86, 'A', 62, ''] 62 [86, 'A', 63, ''] 63 [86, 'A', 64, ''] 64 [86, 'A', 65, ''] 65 [86, 'A', 66, ''] 66 [86, 'A', 67, ''] 67 [86, 'A', 68, ''] 68 [86, 'A', 69, ''] 69 [86, 'A', 70, ''] 70 [86, 'A', 71, ''] 71 [86, 'A', 72, ''] 72 [86, 'A', 73, ''] 73 [86, 'A', 74, ''] 74 [86, 'A', 75, ''] 75 [86, 'A', 76, ''] 76 [86, 'A', 77, ''] 77 [86, 'A', 78, ''] 78 [86, 'A', 79, ''] 79 [86, 'A', 80, ''] 80 [86, 'A', 81, ''] 81 [86, 'A', 82, ''] 82 [86, 'A', 83, ''] 83 [86, 'A', 84, ''] 84 [86, 'A', 85, ''] 85 [86, 'A', 86, ''] 86 [86, 'A', 87, ''] 87 [86, 'A', 88, ''] 88 [86, 'A', 89, ''] 89 [86, 'A', 90, ''] 90 [86, 'A', 91, ''] 91 [86, 'A', 92, ''] 92 [86, 'A', 93, ''] 93 [86, 'B', 1, ''] 94 [86, 'B', 2, ''] 95 [86, 'B', 3, ''] 96 [86, 'B', 4, ''] 97 [86, 'B', 5, ''] 98 [86, 'B', 6, ''] 99 [86, 'B', 7, ''] 100 [86, 'B', 8, ''] 101 [86, 'B', 9, ''] 102 [86, 'B', 10, ''] 103 [86, 'B', 11, ''] 104 [86, 'B', 12, ''] 105 [86, 'B', 13, ''] 106 [86, 'B', 14, ''] 107 [86, 'B', 15, ''] 108 [86, 'B', 16, ''] 109 [86, 'B', 17, ''] 110 [86, 'B', 18, ''] 111 [86, 'B', 19, ''] 112 [86, 'B', 20, ''] 113 [86, 'B', 21, ''] 114 [86, 'B', 22, ''] 115 [86, 'B', 23, ''] 116 [86, 'B', 24, ''] 117 [86, 'B', 25, ''] 118 [86, 'B', 26, ''] 119 [86, 'B', 27, ''] 120 [86, 'B', 28, ''] 121 [86, 'B', 29, ''] 122 [86, 'B', 30, ''] 123 [86, 'B', 31, ''] 124 [86, 'B', 32, ''] 125 [86, 'B', 33, ''] 126 [86, 'B', 34, ''] 127 [86, 'B', 35, ''] 128 [86, 'B', 36, ''] 129 [86, 'B', 37, ''] 130 [86, 'B', 38, ''] 131 [86, 'B', 39, ''] 132 [86, 'B', 40, ''] 133 [86, 'B', 41, ''] 134 [86, 'B', 42, ''] 135 [86, 'B', 43, ''] 136 [86, 'B', 44, ''] 137 [86, 'B', 45, ''] 138 [86, 'B', 46, ''] 139 [86, 'B', 47, ''] 140 [86, 'B', 48, ''] 141 [86, 'B', 49, ''] 142 [86, 'B', 50, ''] 143 [86, 'B', 51, ''] 144 [86, 'B', 52, ''] 145 [86, 'B', 53, ''] 146 [86, 'B', 54, ''] 147 [86, 'B', 55, ''] 148 [86, 'B', 56, ''] 149 [86, 'B', 57, ''] 150 [86, 'B', 58, ''] 151 [86, 'B', 59, ''] 152 [86, 'B', 60, ''] 153 [86, 'B', 61, ''] 154 [86, 'B', 62, ''] 155 [86, 'B', 63, ''] 156 [86, 'B', 64, ''] 157 [86, 'B', 65, ''] 158 [86, 'B', 66, ''] 159 [86, 'B', 67, ''] 160 [86, 'B', 68, ''] 161 [86, 'B', 69, ''] 162 [86, 'B', 70, ''] 163 [86, 'B', 71, ''] 164 [86, 'B', 72, ''] 165 [86, 'B', 73, ''] 166 [86, 'B', 74, ''] 167 [86, 'B', 75, ''] 168 [86, 'B', 76, ''] 169 [86, 'B', 77, ''] 170 [86, 'B', 78, ''] 171 [86, 'B', 79, ''] 172 [86, 'B', 80, ''] 173 [86, 'B', 81, ''] 174 [86, 'B', 82, ''] 175 [86, 'B', 83, ''] 176 [86, 'B', 84, ''] 177 [86, 'B', 85, ''] 178 [86, 'B', 86, ''] 179 [86, 'B', 87, ''] 180 [86, 'B', 88, ''] 181 [86, 'B', 89, ''] 182 [86, 'B', 90, ''] 183 [86, 'B', 91, ''] 184 [86, 'B', 92, ''] 185 [86, 'B', 93, ''] 186 [86, 'B', 94, ''] 187 [86, 'B', 95, ''] 188 [86, 'B', 96, ''] ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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:: Command: (n-chains 87) INFO:: Command: (chain_id 87 0) INFO:: Command: (chain_id 87 1) INFO:: Command: (seqnum-from-serial-number 87 "A" 0) INFO:: Command: (insertion-code-from-serial-number 87 "A" 0) INFO:: Command: (seqnum-from-serial-number 87 "A" 1) INFO:: Command: (insertion-code-from-serial-number 87 "A" 1) INFO:: Command: (seqnum-from-serial-number 87 "A" 2) INFO:: Command: (insertion-code-from-serial-number 87 "A" 2) INFO:: Command: (seqnum-from-serial-number 87 "A" 3) INFO:: Command: (insertion-code-from-serial-number 87 "A" 3) INFO:: Command: (seqnum-from-serial-number 87 "A" 4) INFO:: Command: (insertion-code-from-serial-number 87 "A" 4) INFO:: Command: (seqnum-from-serial-number 87 "A" 5) INFO:: Command: (insertion-code-from-serial-number 87 "A" 5) INFO:: Command: (seqnum-from-serial-number 87 "A" 6) INFO:: Command: (insertion-code-from-serial-number 87 "A" 6) INFO:: Command: (seqnum-from-serial-number 87 "A" 7) INFO:: Command: (insertion-code-from-serial-number 87 "A" 7) INFO:: Command: (seqnum-from-serial-number 87 "A" 8) INFO:: Command: (insertion-code-from-serial-number 87 "A" 8) INFO:: Command: (seqnum-from-serial-number 87 "A" 9) INFO:: Command: (insertion-code-from-serial-number 87 "A" 9) INFO:: Command: (seqnum-from-serial-number 87 "A" 10) INFO:: Command: (insertion-code-from-serial-number 87 "A" 10) INFO:: Command: (seqnum-from-serial-number 87 "A" 11) INFO:: Command: (insertion-code-from-serial-number 87 "A" 11) INFO:: Command: (seqnum-from-serial-number 87 "A" 12) INFO:: Command: (insertion-code-from-serial-number 87 "A" 12) INFO:: Command: (seqnum-from-serial-number 87 "A" 13) INFO:: Command: (insertion-code-from-serial-number 87 "A" 13) INFO:: Command: (seqnum-from-serial-number 87 "A" 14) INFO:: Command: (insertion-code-from-serial-number 87 "A" 14) INFO:: Command: (seqnum-from-serial-number 87 "A" 15) INFO:: Command: (insertion-code-from-serial-number 87 "A" 15) INFO:: Command: (seqnum-from-serial-number 87 "A" 16) INFO:: Command: (insertion-code-from-serial-number 87 "A" 16) INFO:: Command: (seqnum-from-serial-number 87 "A" 17) INFO:: Command: (insertion-code-from-serial-number 87 "A" 17) INFO:: Command: (seqnum-from-serial-number 87 "A" 18) INFO:: Command: (insertion-code-from-serial-number 87 "A" 18) INFO:: Command: (seqnum-from-serial-number 87 "A" 19) INFO:: Command: (insertion-code-from-serial-number 87 "A" 19) INFO:: Command: (seqnum-from-serial-number 87 "A" 20) INFO:: Command: (insertion-code-from-serial-number 87 "A" 20) INFO:: Command: (seqnum-from-serial-number 87 "A" 21) INFO:: Command: (insertion-code-from-serial-number 87 "A" 21) INFO:: Command: (seqnum-from-serial-number 87 "A" 22) INFO:: Command: (insertion-code-from-serial-number 87 "A" 22) INFO:: Command: (seqnum-from-serial-number 87 "A" 23) INFO:: Command: (insertion-code-from-serial-number 87 "A" 23) INFO:: Command: (seqnum-from-serial-number 87 "A" 24) INFO:: Command: (insertion-code-from-serial-number 87 "A" 24) INFO:: Command: (seqnum-from-serial-number 87 "A" 25) INFO:: Command: (insertion-code-from-serial-number 87 "A" 25) INFO:: Command: (seqnum-from-serial-number 87 "A" 26) INFO:: Command: (insertion-code-from-serial-number 87 "A" 26) INFO:: Command: (seqnum-from-serial-number 87 "A" 27) INFO:: Command: (insertion-code-from-serial-number 87 "A" 27) INFO:: Command: (seqnum-from-serial-number 87 "A" 28) INFO:: Command: (insertion-code-from-serial-number 87 "A" 28) INFO:: Command: (seqnum-from-serial-number 87 "A" 29) INFO:: Command: (insertion-code-from-serial-number 87 "A" 29) INFO:: Command: (seqnum-from-serial-number 87 "A" 30) INFO:: Command: (insertion-code-from-serial-number 87 "A" 30) INFO:: Command: (seqnum-from-serial-number 87 "A" 31) INFO:: Command: (insertion-code-from-serial-number 87 "A" 31) INFO:: Command: (seqnum-from-serial-number 87 "A" 32) INFO:: Command: (insertion-code-from-serial-number 87 "A" 32) INFO:: Command: (seqnum-from-serial-number 87 "A" 33) INFO:: Command: (insertion-code-from-serial-number 87 "A" 33) INFO:: Command: (seqnum-from-serial-number 87 "A" 34) INFO:: Command: (insertion-code-from-serial-number 87 "A" 34) INFO:: Command: (seqnum-from-serial-number 87 "A" 35) INFO:: Command: (insertion-code-from-serial-number 87 "A" 35) INFO:: Command: (seqnum-from-serial-number 87 "A" 36) INFO:: Command: (insertion-code-from-serial-number 87 "A" 36) INFO:: Command: (seqnum-from-serial-number 87 "A" 37) INFO:: Command: (insertion-code-from-serial-number 87 "A" 37) INFO:: Command: (seqnum-from-serial-number 87 "A" 38) INFO:: Command: (insertion-code-from-serial-number 87 "A" 38) INFO:: Command: (seqnum-from-serial-number 87 "A" 39) INFO:: Command: (insertion-code-from-serial-number 87 "A" 39) INFO:: Command: (seqnum-from-serial-number 87 "A" 40) INFO:: Command: (insertion-code-from-serial-number 87 "A" 40) INFO:: Command: (seqnum-from-serial-number 87 "A" 41) INFO:: Command: (insertion-code-from-serial-number 87 "A" 41) INFO:: Command: (seqnum-from-serial-number 87 "A" 42) INFO:: Command: (insertion-code-from-serial-number 87 "A" 42) INFO:: Command: (seqnum-from-serial-number 87 "A" 43) INFO:: Command: (insertion-code-from-serial-number 87 "A" 43) INFO:: Command: (seqnum-from-serial-number 87 "A" 44) INFO:: Command: (insertion-code-from-serial-number 87 "A" 44) INFO:: Command: (seqnum-from-serial-number 87 "A" 45) INFO:: Command: (insertion-code-from-serial-number 87 "A" 45) INFO:: Command: (seqnum-from-serial-number 87 "A" 46) INFO:: Command: (insertion-code-from-serial-number 87 "A" 46) INFO:: Command: (seqnum-from-serial-number 87 "A" 47) INFO:: Command: (insertion-code-from-serial-number 87 "A" 47) INFO:: Command: (seqnum-from-serial-number 87 "A" 48) INFO:: Command: (insertion-code-from-serial-number 87 "A" 48) INFO:: Command: (seqnum-from-serial-number 87 "A" 49) INFO:: Command: (insertion-code-from-serial-number 87 "A" 49) INFO:: Command: (seqnum-from-serial-number 87 "A" 50) INFO:: Command: (insertion-code-from-serial-number 87 "A" 50) INFO:: Command: (seqnum-from-serial-number 87 "A" 51) INFO:: Command: (insertion-code-from-serial-number 87 "A" 51) INFO:: Command: (seqnum-from-serial-number 87 "A" 52) INFO:: Command: (insertion-code-from-serial-number 87 "A" 52) INFO:: Command: (seqnum-from-serial-number 87 "A" 53) INFO:: Command: (insertion-code-from-serial-number 87 "A" 53) INFO:: Command: (seqnum-from-serial-number 87 "A" 54) INFO:: Command: (insertion-code-from-serial-number 87 "A" 54) INFO:: Command: (seqnum-from-serial-number 87 "A" 55) INFO:: Command: (insertion-code-from-serial-number 87 "A" 55) INFO:: Command: (seqnum-from-serial-number 87 "A" 56) INFO:: Command: 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(insertion-code-from-serial-number 87 "B" 31) INFO:: Command: (seqnum-from-serial-number 87 "B" 32) INFO:: Command: (insertion-code-from-serial-number 87 "B" 32) INFO:: Command: (seqnum-from-serial-number 87 "B" 33) INFO:: Command: (insertion-code-from-serial-number 87 "B" 33) INFO:: Command: (seqnum-from-serial-number 87 "B" 34) INFO:: Command: (insertion-code-from-serial-number 87 "B" 34) INFO:: Command: (seqnum-from-serial-number 87 "B" 35) INFO:: Command: (insertion-code-from-serial-number 87 "B" 35) INFO:: Command: (seqnum-from-serial-number 87 "B" 36) INFO:: Command: (insertion-code-from-serial-number 87 "B" 36) INFO:: Command: (seqnum-from-serial-number 87 "B" 37) INFO:: Command: (insertion-code-from-serial-number 87 "B" 37) INFO:: Command: (seqnum-from-serial-number 87 "B" 38) INFO:: Command: (insertion-code-from-serial-number 87 "B" 38) INFO:: Command: (seqnum-from-serial-number 87 "B" 39) INFO:: Command: (insertion-code-from-serial-number 87 "B" 39) INFO:: Command: 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(insertion-code-from-serial-number 87 "B" 65) INFO:: Command: (seqnum-from-serial-number 87 "B" 66) INFO:: Command: (insertion-code-from-serial-number 87 "B" 66) INFO:: Command: (seqnum-from-serial-number 87 "B" 67) INFO:: Command: (insertion-code-from-serial-number 87 "B" 67) INFO:: Command: (seqnum-from-serial-number 87 "B" 68) INFO:: Command: (insertion-code-from-serial-number 87 "B" 68) INFO:: Command: (seqnum-from-serial-number 87 "B" 69) INFO:: Command: (insertion-code-from-serial-number 87 "B" 69) INFO:: Command: (seqnum-from-serial-number 87 "B" 70) INFO:: Command: (insertion-code-from-serial-number 87 "B" 70) INFO:: Command: (seqnum-from-serial-number 87 "B" 71) INFO:: Command: (insertion-code-from-serial-number 87 "B" 71) INFO:: Command: (seqnum-from-serial-number 87 "B" 72) INFO:: Command: (insertion-code-from-serial-number 87 "B" 72) INFO:: Command: (seqnum-from-serial-number 87 "B" 73) INFO:: Command: (insertion-code-from-serial-number 87 "B" 73) INFO:: Command: 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(seqnum-from-serial-number 87 "B" 91) INFO:: Command: (insertion-code-from-serial-number 87 "B" 91) INFO:: Command: (seqnum-from-serial-number 87 "B" 92) INFO:: Command: (insertion-code-from-serial-number 87 "B" 92) INFO:: Command: (seqnum-from-serial-number 87 "B" 93) INFO:: Command: (insertion-code-from-serial-number 87 "B" 93) INFO:: Command: (seqnum-from-serial-number 87 "B" 94) INFO:: Command: (insertion-code-from-serial-number 87 "B" 94) INFO:: Command: (seqnum-from-serial-number 87 "B" 95) INFO:: Command: (insertion-code-from-serial-number 87 "B" 95) specs: 189 [[87, 'A', 1, ''], [87, 'A', 2, ''], [87, 'A', 3, ''], [87, 'A', 4, ''], [87, 'A', 5, ''], [87, 'A', 6, ''], [87, 'A', 7, ''], [87, 'A', 8, ''], [87, 'A', 9, ''], [87, 'A', 10, ''], [87, 'A', 11, ''], [87, 'A', 12, ''], [87, 'A', 13, ''], [87, 'A', 14, ''], [87, 'A', 15, ''], [87, 'A', 16, ''], [87, 'A', 17, ''], [87, 'A', 18, ''], [87, 'A', 19, ''], [87, 'A', 20, ''], [87, 'A', 21, ''], [87, 'A', 22, ''], [87, 'A', 23, ''], [87, 'A', 24, ''], [87, 'A', 25, ''], [87, 'A', 26, ''], [87, 'A', 27, ''], [87, 'A', 28, ''], [87, 'A', 29, ''], [87, 'A', 30, ''], [87, 'A', 31, ''], [87, 'A', 32, ''], [87, 'A', 33, ''], [87, 'A', 34, ''], [87, 'A', 35, ''], [87, 'A', 36, ''], [87, 'A', 37, ''], [87, 'A', 38, ''], [87, 'A', 39, ''], [87, 'A', 40, ''], [87, 'A', 41, ''], [87, 'A', 42, ''], [87, 'A', 43, ''], [87, 'A', 44, ''], [87, 'A', 45, ''], [87, 'A', 46, ''], [87, 'A', 47, ''], [87, 'A', 48, ''], [87, 'A', 49, ''], [87, 'A', 50, ''], [87, 'A', 51, ''], [87, 'A', 52, ''], [87, 'A', 53, ''], [87, 'A', 54, ''], [87, 'A', 55, ''], [87, 'A', 56, ''], [87, 'A', 57, ''], [87, 'A', 58, ''], [87, 'A', 59, ''], [87, 'A', 60, ''], [87, 'A', 61, ''], [87, 'A', 62, ''], [87, 'A', 63, ''], [87, 'A', 64, ''], [87, 'A', 65, ''], [87, 'A', 66, ''], [87, 'A', 67, ''], [87, 'A', 68, ''], [87, 'A', 69, ''], [87, 'A', 70, ''], [87, 'A', 71, ''], [87, 'A', 72, ''], [87, 'A', 73, ''], [87, 'A', 74, ''], [87, 'A', 75, ''], [87, 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'B', 36, ''], [87, 'B', 37, ''], [87, 'B', 38, ''], [87, 'B', 39, ''], [87, 'B', 40, ''], [87, 'B', 41, ''], [87, 'B', 42, ''], [87, 'B', 43, ''], [87, 'B', 44, ''], [87, 'B', 45, ''], [87, 'B', 46, ''], [87, 'B', 47, ''], [87, 'B', 48, ''], [87, 'B', 49, ''], [87, 'B', 50, ''], [87, 'B', 51, ''], [87, 'B', 52, ''], [87, 'B', 53, ''], [87, 'B', 54, ''], [87, 'B', 55, ''], [87, 'B', 56, ''], [87, 'B', 57, ''], [87, 'B', 58, ''], [87, 'B', 59, ''], [87, 'B', 60, ''], [87, 'B', 61, ''], [87, 'B', 62, ''], [87, 'B', 63, ''], [87, 'B', 64, ''], [87, 'B', 65, ''], [87, 'B', 66, ''], [87, 'B', 67, ''], [87, 'B', 68, ''], [87, 'B', 69, ''], [87, 'B', 70, ''], [87, 'B', 71, ''], [87, 'B', 72, ''], [87, 'B', 73, ''], [87, 'B', 74, ''], [87, 'B', 75, ''], [87, 'B', 76, ''], [87, 'B', 77, ''], [87, 'B', 78, ''], [87, 'B', 79, ''], [87, 'B', 80, ''], [87, 'B', 81, ''], [87, 'B', 82, ''], [87, 'B', 83, ''], [87, 'B', 84, ''], [87, 'B', 85, ''], [87, 'B', 86, ''], [87, 'B', 87, ''], [87, 'B', 88, ''], [87, 'B', 89, ''], [87, 'B', 90, ''], [87, 'B', 91, ''], [87, 'B', 92, ''], [87, 'B', 93, ''], [87, 'B', 94, ''], [87, 'B', 95, ''], [87, 'B', 96, '']] ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2goz-manip.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2goz-manip.pdb PDB file /lmb/home/pemsley/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links INFO:: NCS chain comparison 10/85 Molecule 88 read successfully DEBUG:: there were 7 types with no dictionary ok test60_0 (__main__.PdbMtzTestFunctions) post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok test61_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... INFO:: Command: (write-pdb-file 0 "rnase_zip_test.pdb.gz") INFO:: Command: (handle-read-draw-molecule-with-recentre "rnase_zip_test.pdb.gz" 1) gzip: stdout: Broken pipe gzip: stdout: Broken pipe INFO:: Reading coordinate file: rnase_zip_test.pdb.gz PDB file rnase_zip_test.pdb.gz has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 89 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 2 CB ok test62_0 (__main__.PdbMtzTestFunctions) Fix for Oliver Clarke fit by atom selection bug ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 90 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.036 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.875045 max: 2.97757 INFO:: 0.004 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.106 seconds for contour map INFO:: 0.162 seconds in total masking....masking done INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:10_2017_modification_0.pdb.gz INFO:: replace_coords: 745 atoms updated. bl: 0.0363730669589 ok test999_0 (__main__.PdbMtzTestFunctions) Renumber residue range without overwriting coordinates. ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 92 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_0.pdb.gz INFO:: Command: (renumber-residue-range 92 "A" 10 20 -55) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_1.pdb.gz INFO:: Command: (renumber-residue-range 92 "A" 90 93 10) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_2.pdb.gz INFO:: Command: (renumber-residue-range 92 "A" 89 91 1) WARNING:: the new residue range overlaps with original one. Please change the range. Nothing has been done. INFO:: Command: (renumber-residue-range 92 "A" 80 91 12) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_3.pdb.gz INFO:: Command: (renumber-residue-range 92 "A" -100 200 9) ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/HOF.RES" 1) SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.9028 13.6977 9.2374 90 98.211 90 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 93 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/HOF.RES") ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/hollander.ins" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.3243 34.3243 11.0887 90 90 90 READ-INS:: Spacegroup: "I 41 2 2" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 94 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/hollander.ins") INFO:: spacegroup: I 41 2 2 ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.726 77.726 77.726 90 90 90 READ-INS:: Spacegroup: "I 21 3" INFO:: chain has 121 residues Symmetry available for this molecule Molecule 95 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/insulin.res") reject uvw = ( 58, 41, 76) rho: 6.07907 implausible (high) INFO:: Map statistics: mean: -7.57023e-05 st.d: 0.304925 INFO:: Map statistics: min: -0.781031 max: 5.15441 Map statistics: mean: -7.57023e-05 st.d: 0.304925 Map statistics: min: -0.781031, max: 5.15441 -0.706838 129 -0.558452 2336 -0.410066 14093 -0.26168 33222 -0.113294 65572 0.0350918 78739 0.183478 27967 0.331864 6373 0.48025 3664 0.628636 2583 0.777022 2083 0.925408 1626 1.07379 1370 1.22218 1012 1.37057 757 1.51895 523 1.66734 337 1.81572 250 1.96411 158 2.1125 95 2.26088 75 2.40927 54 2.55765 42 2.70604 15 2.85442 14 3.00281 15 3.1512 7 3.29958 7 3.44797 7 3.59635 1 3.74474 1 3.89313 7 4.04151 4 4.1899 3 4.33828 3 4.48667 0 4.63506 2 4.78344 1 4.93183 1 5.08021 1 5.2286 0 INFO:: Map statistics: mean: -1.00548e-05 st.d: 0.0468085 INFO:: Map statistics: min: -0.211523 max: 0.648623 Map statistics: mean: -1.00548e-05 st.d: 0.0468085 Map statistics: min: -0.211523, max: 0.648623 -0.200772 7 -0.179268 48 -0.157764 209 -0.136261 787 -0.114757 2257 -0.0932533 5676 -0.0717496 12730 -0.050246 24380 -0.0287423 38191 -0.00723865 46229 0.014265 43880 0.0357687 32484 0.0572724 19420 0.078776 9718 0.10028 4120 0.121783 1677 0.143287 718 0.164791 329 0.186294 133 0.207798 77 0.229302 29 0.250805 11 0.272309 13 0.293813 8 0.315316 2 0.33682 2 0.358324 2 0.379827 1 0.401331 1 0.422835 2 0.444338 2 0.465842 1 0.487346 1 0.508849 1 0.530353 1 0.551857 1 0.57336 0 0.594864 0 0.616368 0 0.637871 2 0.659375 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... WARNING:: invalid molecule (204050) for write_shelx_ins_file WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... INFO:: Command: (update-go-to-atom-window-on-new-mol) ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... INFO:: Command: (update-go-to-atom-window-on-new-mol) INFO:: Masking around 32 atoms fitting terminal residue with 1000 random trials --- in best_fit_phi_psi() with offset 1 INFO:: Fitting terminal residue without individual rigid body fitting. --- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000 called fit_terminal_residue_generic() residue-seqnum: 2020 offset: 1 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Wed_Aug__2_00:52:16_2017_modification_0.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CD2" INFO:: Command: (add-terminal-residue 99 "B" 2020 1) ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... INFO:: Command: (set-rotation-centre 3.00 -1.00 60.00) INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Wed_Aug__2_00:52:16_2017_modification_0.res 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule INFO:: Command: (place-typed-atom-at-pointer "Water") INFO:: Command: (resname-from-serial-number 95 "D" 68) INFO:: Command: (seqnum-from-serial-number 95 "D" 68) INFO:: Command: (insertion-code-from-serial-number 95 "D" 68) ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... INFO:: Command: (n-chains 95) 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 0.304925 INFO:: Using density cut-off: 0.182955 (0.6 sigma) (mean -0.0203497 stdev: 0.111926) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4 3.2 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.856, 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, 8.133, 53.25) is too big to be water INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water INFO:: found 28 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Wed_Aug__2_00:52:16_2017_modification_1.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O " INFO:: Adding to solvent chain: D INFO:: Command: (n-chains 95) INFO:: Command: (resname-from-serial-number 95 "D" 96) INFO:: Command: (seqnum-from-serial-number 95 "D" 96) INFO:: Command: (insertion-code-from-serial-number 95 "D" 96) ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/miller/shelx-test4-NPD-mini.res" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.14 83.03 89.79 90 90 90 READ-INS:: Spacegroup: "P 21 21 21" INFO:: chain has 5 residues Symmetry available for this molecule Molecule 100 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/miller/shelx-test4-NPD-mini.res") INFO:: Command: (close-molecule 100) ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... INFO:: Command: (close-molecule 96) INFO:: Command: (close-molecule 95) ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/horma-p21.res" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 101 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/horma-p21.res") INFO:: SHELXL file new-horma.ins written. INFO:: Command: (handle-read-draw-molecule-with-recentre "new-horma.ins" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 102 read successfully INFO:: Command: (read-shelx-ins-file "new-horma.ins") b_1: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] b_2: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066] ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/crash.hat" 0) LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.999 108.999 107.555 90 90 90 READ-INS:: Spacegroup: "I 4 2 2" INFO:: chain has 4 residues Symmetry available for this molecule Molecule 103 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/crash.hat") INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/crash.hat" 1) LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 108.999 108.999 107.555 90 90 90 READ-INS:: Spacegroup: "I 4 2 2" INFO:: chain has 4 residues Symmetry available for this molecule Molecule 104 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/crash.hat") ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 0) INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb PDB file coot-ccp4/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 105 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:16_2017_modification_0.pdb.gz ::: add_cif_dictionary() called with coot-ccp4/libcheck_3GP.cif -999999 0 Welcome to Coot INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:16_2017_modification_1.pdb.gz INFO:: Command: (delete-residue-hydrogens 105 "A" 1 "" "") ok test02_0 (__main__.LigandTestFunctions) Set Bond thickness test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 106 read successfully DEBUG:: there were 0 types with no dictionary here 1 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Wed_Aug__2_00:52:20_2017_modification_0.pdb.gz ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-LIG.pdb PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 107 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-LIG.pdb PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 108 read successfully DEBUG:: there were 1 types with no dictionary INFO:: comp-id: LIG is marked for non-autoloading - stopping now WARNING:: can't find LIG in monomer dictionary ok test05_0 (__main__.LigandTestFunctions) Move and Refine Ligand test ... INFO:: Command: (go-to-view-number 2 1) INFO:: Command: (set-rotation-centre 55.30 9.10 20.60) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:16_2017_modification_2.pdb.gz INFO:: Command: (backup-state 105) INFO:: Command: (turn-off-backup 105) ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Command: (turn-on-backup 105) ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 0) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 109 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (copy-molecule 109) INFO:: Command: (copy-molecule 109) INFO:: Command: (copy-molecule 109) INFO:: Command: (copy-molecule 109) INFO:: Command: (copy-molecule 109) INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /lmb/home/pemsley/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 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 0/113 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 0/117 INFO:: fill_ghost_info Constructed 6 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain A" Ghost 1 name: "NCS found from matching Chain E onto Chain A" Ghost 2 name: "NCS found from matching Chain G onto Chain A" Ghost 3 name: "NCS found from matching Chain D onto Chain B" Ghost 4 name: "NCS found from matching Chain F onto Chain B" Ghost 5 name: "NCS found from matching Chain H onto Chain B" Molecule 115 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making conventional map from MTZ filename /lmb/home/pemsley/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:: 0.145 seconds to read MTZ file INFO:: 0.097 seconds to initialize map INFO:: 0.066 seconds for FFT INFO:: Map statistics: mean: -8.79003e-07 st.d: 0.171188 INFO:: Map statistics: min: -0.695441 max: 1.34304 INFO:: 0.021 seconds for statistics Map mean: ........ -8.79003e-07 Map sigma: ....... 0.171188 Map maximum: ..... 1.34304 Map minimum: ..... -0.695441 INFO:: 0.04 seconds for contour map INFO:: 0.369 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: making difference map from MTZ filename /lmb/home/pemsley/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:: 0.093 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.067 seconds for FFT INFO:: Map statistics: mean: 2.0939e-06 st.d: 0.0333923 INFO:: Map statistics: min: -0.191665 max: 0.366077 INFO:: 0.021 seconds for statistics Map mean: ........ 2.0939e-06 Map sigma: ....... 0.0333923 Map maximum: ..... 0.366077 Map minimum: ..... -0.191665 INFO:: 0.015 seconds for contour map INFO:: 0.198 seconds in total INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "DELFWT" "PHDELWT" "" 0 1 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) INFO:: ligand number 0 is molecule number 109 with wiggly flag: 0 in execute_ligand_search_internal() import maps from mol 116 INFO:: Protein centre at: xyz = ( 58.29, 34.65, 30.63) INFO:: Map statistics: mean: -0.0216745 st.d: 0.0886263 INFO:: Map statistics: min: -0.695441 max: 0.754209 Map statistics: mean: -0.0216745 st.d: 0.0886263 Map statistics: min: -0.695441, max: 0.754209 -0.67732 6 -0.641079 8 -0.604838 27 -0.568596 116 -0.532355 354 -0.496114 977 -0.459873 1943 -0.423631 3356 -0.38739 5156 -0.351149 6576 -0.314908 7850 -0.278666 8875 -0.242425 9742 -0.206184 11742 -0.169943 16950 -0.133701 29805 -0.0974601 58214 -0.0612189 102888 -0.0249776 143000 0.0112636 471775 0.0475049 106846 0.0837461 56087 0.119987 21597 0.156229 6911 0.19247 2135 0.228711 920 0.264952 467 0.301194 346 0.337435 216 0.373676 118 0.409917 117 0.446159 80 0.4824 50 0.518641 28 0.554882 33 0.591124 15 0.627365 14 0.663606 11 0.699847 2 0.736089 6 0.77233 1 INFO:: find_clusters map_rms is 0.171132 INFO:: Using density cut-off: 0.171132 (1 sigma) (mean -0.0216776 stdev: 0.0886191) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4 3.2 INFO:: Finding clusters...done debug:: n_ligands_for_cluster() top_score 4.04177 and 4 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 2.0066 and 9 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 2.09237 and 4 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 1.85663 and 6 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 1.38681 and 10 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 1.61147 and 8 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 2.10047 and 8 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 1.69083 and 7 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 2.12333 and 2 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring debug:: n_ligands_for_cluster() top_score 1.84146 and 6 are decent out of 12 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring Fitting NPO gave these results: [119, 120, 121, 122, 123, 124, 125, 126, 127, 128] ok test07_0 (__main__.LigandTestFunctions) Flip residue (around eigen vectors) ... INFO:: Command: (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 1) INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb PDB file coot-ccp4/monomer-3GP.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Molecule 129 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (copy-molecule 129) INFO:: Command: (set-go-to-atom-molecule 129) INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:53_2017_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_Wed_Aug__2_00:52:53_2017_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:53_2017_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:53_2017_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. distance d2: 1.60332907424e-07 ok test08_0 (__main__.LigandTestFunctions) Test dipole ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/dipole-residues.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/dipole-residues.pdb PDB file /lmb/home/pemsley/data/greg-data/dipole-residues.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model Molecule 131 read successfully DEBUG:: there were 0 types with no dictionary info:: dipole components [-2.219999939203263, 4.440892098500626e-16, 0.0] ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... ::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif -999999 0 WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints ::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif -999999 0 WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints ::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif -999999 0 WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints ok test10_0 (__main__.LigandTestFunctions) Pyrogen Runs OK? ... ok test11_0 (__main__.LigandTestFunctions) pyrogen dictionary does not make double-quoted atom names ... ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 132 read successfully DEBUG:: there were 0 types with no dictionary storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 132 INFO:: Command: (assign-pir-sequence 132 "A" ">test ACDEFGHIKLMNPQ*") debug seq ACDEFGHIKLMNPQ storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 132 INFO:: Command: (assign-pir-sequence 132 "A" ">test ACDEFGHIKLMNPQRST*") ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb PDB file /lmb/home/pemsley/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 INFO:: NCS chain comparison 1/2 INFO:: NCS chain comparison 0/2 INFO:: NCS chain comparison 0/13 Molecule 133 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.013 seconds for FFT INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501 INFO:: Map statistics: min: -0.875045 max: 2.97757 INFO:: 0.004 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.076 seconds for contour map INFO:: 0.119 seconds in total storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 133 INFO:: Command: (assign-pir-sequence 133 "A" "> tutorial-modern chain A RNASE DVSGTVCLSA LPPEATDTLN LIASDGPFPY SQDGVVFQNR ESVLPTQSYG YYHEYTVITP GARTRGTRRI ICGEATQEDY YTGDHYATFS LID * ") INFO:: Command: (set-rotation-centre 64.27 7.04 14.42) Cootaneering: imol 133 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/_lmb_home_pemsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Wed_Aug__2_00:53:07_2017_modification_0.pdb.gz bypassing ? at 0 Mutating to GLU at 1 Mutating poly_ala residue number 58 Mutating to TYR at 2 Mutating poly_ala residue number 59 Mutating to THR at 3 Mutating poly_ala residue number 60 Mutating to VAL at 4 Mutating poly_ala residue number 61 Mutating to ILE at 5 Mutating poly_ala residue number 62 Mutating to THR at 6 Mutating poly_ala residue number 63 Mutating to PRO at 7 Mutating poly_ala residue number 64 Mutating to GLY at 8 Mutating poly_ala residue number 65 Mutating to ALA at 9 Mutating poly_ala residue number 66 Mutating to ARG at 10 Mutating poly_ala residue number 67 Mutating to THR at 11 Mutating poly_ala residue number 68 Mutating to ARG at 12 Mutating poly_ala residue number 69 DEBUG:: Creating a new chain B WARNING:: no rotamers probabilities for residue type GLY INFO:: replace_coords: 9 atoms updated. oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: replace_coords: 12 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 8 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 7 atoms updated. WARNING:: no rotamers probabilities for residue type GLY WARNING:: no rotamers probabilities for residue type ALA INFO:: replace_coords: 11 atoms updated. INFO:: replace_coords: 7 atoms updated. INFO:: replace_coords: 11 atoms updated. ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:53:08_2017_modification_0.pdb.gz INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: Command: (copy-molecule 135) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) INFO:: Command: (set-rotation-centre 76.27 10.04 14.42) INFO:: Command: (go-to-view-number 3 1) INFO:: Command: (n-chains 136) INFO:: Command: (chain_id 136 0) INFO:: Command: (chain_id 136 1) INFO:: Command: (is-solvent-chain-p 136 "A") There are 8 residues in chain A INFO:: Command: (resname-from-serial-number 136 "A" 0) INFO:: Command: (seqnum-from-serial-number 136 "A" 0) INFO:: Command: (insertion-code-from-serial-number 136 "A" 0) INFO:: Command: (resname-from-serial-number 136 "A" 1) INFO:: Command: (seqnum-from-serial-number 136 "A" 1) INFO:: Command: (insertion-code-from-serial-number 136 "A" 1) INFO:: Command: (resname-from-serial-number 136 "A" 2) INFO:: Command: (seqnum-from-serial-number 136 "A" 2) INFO:: Command: (insertion-code-from-serial-number 136 "A" 2) INFO:: Command: (resname-from-serial-number 136 "A" 3) INFO:: Command: (seqnum-from-serial-number 136 "A" 3) INFO:: Command: (insertion-code-from-serial-number 136 "A" 3) INFO:: Command: (resname-from-serial-number 136 "A" 4) INFO:: Command: (seqnum-from-serial-number 136 "A" 4) INFO:: Command: (insertion-code-from-serial-number 136 "A" 4) INFO:: Command: (resname-from-serial-number 136 "A" 5) INFO:: Command: (seqnum-from-serial-number 136 "A" 5) INFO:: Command: (insertion-code-from-serial-number 136 "A" 5) INFO:: Command: (resname-from-serial-number 136 "A" 6) INFO:: Command: (seqnum-from-serial-number 136 "A" 6) INFO:: Command: (insertion-code-from-serial-number 136 "A" 6) INFO:: Command: (resname-from-serial-number 136 "A" 7) INFO:: Command: (seqnum-from-serial-number 136 "A" 7) INFO:: Command: (insertion-code-from-serial-number 136 "A" 7) INFO:: Command: (is-solvent-chain-p 136 "B") There are 8 residues in chain B INFO:: Command: (resname-from-serial-number 136 "B" 0) INFO:: Command: (seqnum-from-serial-number 136 "B" 0) INFO:: Command: (insertion-code-from-serial-number 136 "B" 0) INFO:: Command: (resname-from-serial-number 136 "B" 1) INFO:: Command: (seqnum-from-serial-number 136 "B" 1) INFO:: Command: (insertion-code-from-serial-number 136 "B" 1) INFO:: Command: (resname-from-serial-number 136 "B" 2) INFO:: Command: (seqnum-from-serial-number 136 "B" 2) INFO:: Command: (insertion-code-from-serial-number 136 "B" 2) INFO:: Command: (resname-from-serial-number 136 "B" 3) INFO:: Command: (seqnum-from-serial-number 136 "B" 3) INFO:: Command: (insertion-code-from-serial-number 136 "B" 3) INFO:: Command: (resname-from-serial-number 136 "B" 4) INFO:: Command: (seqnum-from-serial-number 136 "B" 4) INFO:: Command: (insertion-code-from-serial-number 136 "B" 4) INFO:: Command: (resname-from-serial-number 136 "B" 5) INFO:: Command: (seqnum-from-serial-number 136 "B" 5) INFO:: Command: (insertion-code-from-serial-number 136 "B" 5) INFO:: Command: (resname-from-serial-number 136 "B" 6) INFO:: Command: (seqnum-from-serial-number 136 "B" 6) INFO:: Command: (insertion-code-from-serial-number 136 "B" 6) INFO:: Command: (resname-from-serial-number 136 "B" 7) INFO:: Command: (seqnum-from-serial-number 136 "B" 7) INFO:: Command: (insertion-code-from-serial-number 136 "B" 7) WARNING:: No symmetry available for this molecule WARNING:: No Symmetry for this model INFO:: Command: (copy-molecule 135) INFO:: Matching/moving molecule number 137 to 137 INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 2.32709e-06 rms devi: 2.52247e-06 max devi: 4.32529e-06 min devi: 5.02443e-07 INFO:: Axis orientation: ( -0.2821, -0.09945, 0.9542) INFO:: Rotation in CCP4 Polar Angles: Polar = ( 0, 0, 0) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Wed_Aug__2_00:53:12_2017_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 1,-2.361e-08,-2.461e-09| | 2.361e-08, 1, 6.979e-09| | 2.461e-09,-6.979e-09, 1| ( -24.01, -24.01, -24.01) No unit cell for this molecule, hence no fractional matrix. INFO:: Command: (go-to-view-number 4 1) ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/1wly.pdb" 0) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1wly.pdb PDB file /lmb/home/pemsley/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Molecule 138 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/1yb5.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1yb5.pdb PDB file /lmb/home/pemsley/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 324/324 INFO:: NCS chain comparison 0/324 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 139 read successfully DEBUG:: there were 2 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: Command: (graphics-to-ca-plus-ligands-representation 138) INFO:: Command: (graphics-to-ca-plus-ligands-representation 139) INFO:: reference 138 has 750 atoms selected INFO:: moving 139 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance(/A) A 6 A 7 A 8 <---> A 2 : 0.7510 A 9 <---> A 3 : 0.9422 A 10 <---> A 4 : 0.6300 A 11 <---> A 5 : 0.7119 A 12 <---> A 6 : 0.6310 A 13 <---> A 7 : 0.4675 A 14 <---> A 8 : 0.4264 A 15 <---> A 9 : 0.9792 A 16 <---> A 10 : 0.7549 A 17 <---> A 11 : 0.4884 A 18 <---> A 12 : 0.7451 A 19 <---> A 13 : 0.4606 A 20 <---> A 14 : 1.2809 A 21 <---> A 15 : 1.2412 A 22 <---> A 16 : 1.0733 A 23 <---> A 17 : 0.9730 A 24 <---> A 18 : 0.4705 A 25 <---> A 19 : 0.3560 A 26 <---> A 20 : 3.1145 A 27 A 28 <---> A 21 : 1.5754 A 29 <---> A 22 : 1.6322 A 30 A 31 <---> A 23 : 1.9973 A 32 <---> A 25 : 1.8324 A 33 <---> A 26 : 0.9310 A 34 <---> A 27 : 0.6808 A 35 <---> A 28 : 0.2674 A 36 <---> A 29 : 0.5995 A 37 <---> A 30 : 0.6992 A 38 <---> A 31 : 0.8620 A 39 <---> A 32 : 0.8421 A 40 <---> A 33 : 0.7208 A 41 <---> A 34 : 0.8681 A 42 <---> A 35 : 0.7781 A 43 <---> A 36 : 0.6211 A 44 <---> A 37 : 0.4657 A 45 <---> A 38 : 0.7475 A 46 <---> A 39 : 0.5170 A 47 <---> A 40 : 0.5058 A 48 <---> A 41 : 0.8897 A 49 <---> A 42 : 0.5835 A 50 <---> A 43 : 0.4347 A 51 <---> A 44 : 0.6192 A 52 <---> A 45 : 0.2150 A 53 <---> A 46 : 0.7474 A 54 <---> A 47 : 1.0213 A 55 <---> A 48 : 0.9208 A 56 <---> A 49 : 0.9392 A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 0.4666 A 66 <---> A 61 : 0.0523 A 67 <---> A 62 : 1.0719 A 68 <---> A 63 : 0.7933 A 69 <---> A 64 : 0.8916 A 70 <---> A 65 : 1.2580 A 71 <---> A 66 : 0.6932 A 72 <---> A 67 : 1.0345 A 73 <---> A 68 : 1.4417 A 74 <---> A 69 : 0.9092 A 75 <---> A 70 : 1.6166 A 76 <---> A 71 : 0.8741 A 77 <---> A 72 : 0.2388 A 78 <---> A 73 : 0.3118 A 79 <---> A 74 : 0.3887 A 80 <---> A 75 : 0.7613 A 81 <---> A 76 : 0.9044 A 82 <---> A 77 : 0.6090 A 83 <---> A 78 : 1.7978 A 84 <---> A 79 : 1.9256 A 85 <---> A 80 : 1.3416 A 86 <---> A 81 : 0.5658 A 87 <---> A 82 : 0.4480 A 88 <---> A 83 : 0.9078 A 89 <---> A 84 : 0.3625 A 90 <---> A 85 : 0.4040 A 91 <---> A 86 : 0.4586 A 92 <---> A 87 : 0.4340 A 93 <---> A 88 : 0.3664 A 94 <---> A 89 : 0.4921 A 95 <---> A 90 : 0.6498 A 96 <---> A 91 : 1.5805 A 97 <---> A 92 : 2.8839 A 98 A 99 A 100 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_1yb5.pdb_Wed_Aug__2_00:53:20_2017_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.9117, -0.3803, 0.1557| | -0.3625, 0.9227, 0.131| | -0.1935, 0.06299, -0.9791| ( 70.65, 7.793, 21.29) Rotation - polar (omega,phi,kappa) 87.1413 101.0220 169.7385 Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277 Translation - Angstroms 70.6538 7.7930 21.2852 INFO: core rmsd achieved: 1.0199 Angstroems number of residues in reference structure: 322 number of residues in moving structure: 324 number of residues in aligned sections (reference): 100 number of residues in aligned sections (moving): 110 number of aligned residues: 95 number of gaps: 4 number of misdirections: 0 number of SSE combinations: 4.0000 sequence identity: 30.5263% INFO:: Command: (set-rotation-centre 65.65 -3.00 -4.00) INFO:: Command: (go-to-view-number 5 1) ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/1pyd.pdb" 0) WARNING:: Error reading /lmb/home/pemsley/data/greg-data/1pyd.pdb INFO:: Command: (graphics-to-ca-plus-ligands-representation -1) INFO:: Command: (set-graphics-window-size 678 452) INFO:: Command: (molecule-name 0) 0 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 1) 1 /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb 2 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 3 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 4) 4 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 5) 5 mainchain INFO:: Command: (molecule-name 6) 6 /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: Command: (molecule-name 7) 7 regression-test-terminal-residue.pdb INFO:: Command: (molecule-name 8) 8 atom selection from regression-test-terminal-residue.pdb INFO:: Command: (molecule-name 9) 9 /lmb/home/pemsley/data/greg-data/frag-2wot.pdb INFO:: Command: (molecule-name 10) 10 sphere selection from tutorial-modern.pdb INFO:: Command: (molecule-name 11) 11 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 13) 13 /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb INFO:: Command: (molecule-name 14) 14 /lmb/home/pemsley/data/greg-data/res098.pdb INFO:: Command: (molecule-name 15) 15 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb 16 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 17) 17 /lmb/home/pemsley/data/greg-data/pdb3knw.ent INFO:: Command: (molecule-name 18) 18 /lmb/home/pemsley/data/greg-data/pdb1py3.ent INFO:: Command: (molecule-name 21) 21 /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb INFO:: Command: (molecule-name 22) 22 /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb INFO:: Command: (molecule-name 23) 23 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb 24 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 25) 25 /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb INFO:: Command: (molecule-name 26) 26 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb 27 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 28) 28 /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb INFO:: Command: (molecule-name 29) 29 /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb INFO:: Command: (molecule-name 30) 30 Copy_of_/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb 31 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT INFO:: Command: (molecule-name 32) 32 /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb INFO:: Command: (molecule-name 33) 33 /lmb/home/pemsley/data/greg-data/val.pdb INFO:: Command: (molecule-name 34) 34 /lmb/home/pemsley/data/greg-data/2yie-frag.pdb INFO:: Command: (molecule-name 35) 35 /lmb/home/pemsley/data/greg-data/4f8g.pdb INFO:: Command: (molecule-name 36) 36 /lmb/home/pemsley/data/greg-data/4f8g.pdb 37 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 38 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 39) 39 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb 40 Generic Masked Map 41 difference-map 44 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 45 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT 46 averaged-map 47 difference-map INFO:: Command: (molecule-name 48) 48 /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb 49 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 50) 50 /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb INFO:: Command: (molecule-name 51) 51 /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb INFO:: Command: (molecule-name 52) 52 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 53) 53 /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 54) 54 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 55) 55 Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 56) 56 atom selection from tutorial-modern.pdb INFO:: Command: (molecule-name 57) 57 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 58) 58 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 59) 59 /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb INFO:: Command: (molecule-name 60) 60 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 61) 61 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 62) 62 /lmb/home/pemsley/data/greg-data/pdb3hfl.ent 63 /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT INFO:: Command: (molecule-name 64) 64 Ideal-A-form-RNA INFO:: Command: (molecule-name 65) 65 Ideal-A-form-RNA INFO:: Command: (molecule-name 66) 66 Ideal-A-form-DNA INFO:: Command: (molecule-name 67) 67 Ideal-A-form-DNA INFO:: Command: (molecule-name 68) 68 Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 69) 69 /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb INFO:: Command: (molecule-name 70) 70 /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb INFO:: Command: (molecule-name 71) 71 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 72) 72 /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb INFO:: Command: (molecule-name 73) 73 /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb INFO:: Command: (molecule-name 74) 74 Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb 75 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 76) 76 Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 77) 77 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 78) 78 /lmb/home/pemsley/data/greg-data/pdb1hvv.ent INFO:: Command: (molecule-name 79) 79 /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb INFO:: Command: (molecule-name 80) 80 /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 81) 81 SymOp_-X,-X+Y,-Z+1/3_Copy_of_78 INFO:: Command: (molecule-name 82) 82 Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 83) 83 Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 84) 84 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 85) 85 /lmb/home/pemsley/data/greg-data/pdb1py3.ent INFO:: Command: (molecule-name 86) 86 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 87) 87 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 88) 88 /lmb/home/pemsley/data/greg-data/2goz-manip.pdb INFO:: Command: (molecule-name 89) 89 rnase_zip_test.pdb.gz INFO:: Command: (molecule-name 90) 90 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb 91 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 92) 92 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 93) 93 /lmb/home/pemsley/data/greg-data/HOF.RES INFO:: Command: (molecule-name 94) 94 /lmb/home/pemsley/data/greg-data/hollander.ins 97 /lmb/home/pemsley/data/greg-data/insulin.fcf Diff-SigmaA INFO:: Command: (molecule-name 98) 98 atom selection from insulin.res INFO:: Command: (molecule-name 99) 99 atom selection from insulin.res INFO:: Command: (molecule-name 101) 101 /lmb/home/pemsley/data/greg-data/horma-p21.res INFO:: Command: (molecule-name 102) 102 new-horma.ins INFO:: Command: (molecule-name 103) 103 /lmb/home/pemsley/data/greg-data/crash.hat INFO:: Command: (molecule-name 104) 104 /lmb/home/pemsley/data/greg-data/crash.hat INFO:: Command: (molecule-name 105) 105 coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 106) 106 /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb INFO:: Command: (molecule-name 107) 107 /lmb/home/pemsley/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 108) 108 /lmb/home/pemsley/data/greg-data/test-LIG.pdb INFO:: Command: (molecule-name 109) 109 /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 110) 110 Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 111) 111 Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 112) 112 Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 113) 113 Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 114) 114 Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb INFO:: Command: (molecule-name 115) 115 /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb 116 /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT 117 /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT 118 Masked (by protein) INFO:: Command: (molecule-name 119) 119 Fitted ligand #0-0 INFO:: Command: (molecule-name 120) 120 Fitted ligand #1-0 INFO:: Command: (molecule-name 121) 121 Fitted ligand #2-0 INFO:: Command: (molecule-name 122) 122 Fitted ligand #3-0 INFO:: Command: (molecule-name 123) 123 Fitted ligand #4-0 INFO:: Command: (molecule-name 124) 124 Fitted ligand #5-0 INFO:: Command: (molecule-name 125) 125 Fitted ligand #6-0 INFO:: Command: (molecule-name 126) 126 Fitted ligand #7-0 INFO:: Command: (molecule-name 127) 127 Fitted ligand #8-0 INFO:: Command: (molecule-name 128) 128 Fitted ligand #9-0 INFO:: Command: (molecule-name 129) 129 coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 130) 130 Copy_of_coot-ccp4/monomer-3GP.pdb INFO:: Command: (molecule-name 131) 131 /lmb/home/pemsley/data/greg-data/dipole-residues.pdb INFO:: Command: (molecule-name 132) 132 /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb INFO:: Command: (molecule-name 133) 133 /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb 134 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT INFO:: Command: (molecule-name 135) 135 Ideal-A-form-RNA INFO:: Command: (molecule-name 136) 136 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 137) 137 Copy_of_Ideal-A-form-RNA INFO:: Command: (molecule-name 138) 138 /lmb/home/pemsley/data/greg-data/1wly.pdb INFO:: Command: (molecule-name 139) 139 /lmb/home/pemsley/data/greg-data/1yb5.pdb INFO:: Command: (graphics-to-ca-plus-ligands-representation 139) ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2qd9.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2qd9.pdb PDB file /lmb/home/pemsley/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Molecule 140 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2gtn.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2gtn.pdb PDB file /lmb/home/pemsley/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 0/337 Molecule 141 read successfully DEBUG:: there were 1 types with no dictionary INFO:: reference 140 has 169 atoms selected INFO:: moving 141 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2gtn.pdb_Wed_Aug__2_00:53:31_2017_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491 Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832 Translation - Angstroms 0.3207 0.6598 0.8819 INFO: core rmsd achieved: 0.2210 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1.0000 sequence identity: 100.0000% ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.0260 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0130 seconds for FFT INFO:: Map statistics: mean: 0.0000 st.d: 0.3115 INFO:: Map statistics: min: -0.8750 max: 2.9776 INFO:: 0.0040 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0770 seconds for contour map INFO:: 0.1200 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) INFO:: Map statistics: mean: 0.0003 st.d: 0.3250 INFO:: Map statistics: min: -1.4894 max: 2.4019 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 87759 -0.1761 106866 -0.0788 105275 0.0185 88484 0.1158 67330 0.2131 50443 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 3 2.4506 1 INFO:: installing ghost map with name :Map 142 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) INFO:: Map statistics: mean: 0.0004 st.d: 0.3236 INFO:: Map statistics: min: -1.4496 max: 2.3411 Map statistics: mean: 0.0004 st.d: 0.3236 Map statistics: min: -1.4496, max: 2.3411 -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 1 2.3885 1 ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... NCS info: [['A', 'B']] ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 21 3" INFO:: chain has 121 residues Symmetry available for this molecule Molecule 147 read successfully INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/insulin.res") no diffs NCS target chain has 93 peers. ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 148 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_0.pdb.gz INFO:: Command: (delete-residue 148 "B" 1 "") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_1.pdb.gz INFO:: Command: (delete-residue 148 "B" 2 "") INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_2.pdb.gz INFO:: Command: (delete-residue 148 "B" 3 "") INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 148 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 148 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_3.pdb.gz INFO:: Command: (seqnum-from-serial-number 148 "B" 0) INFO:: Command: (seqnum-from-serial-number 148 "B" 1) INFO:: Command: (seqnum-from-serial-number 148 "B" 2) INFO:: Command: (seqnum-from-serial-number 148 "B" 3) INFO:: Command: (seqnum-from-serial-number 148 "B" 4) INFO:: Command: (seqnum-from-serial-number 148 "B" 5) INFO:: Command: (seqnum-from-serial-number 148 "B" 6) INFO:: Command: (seqnum-from-serial-number 148 "B" 7) INFO:: Command: (seqnum-from-serial-number 148 "B" 8) INFO:: Command: (seqnum-from-serial-number 148 "B" 9) INFO:: Command: (seqnum-from-serial-number 148 "B" 10) INFO:: Command: (seqnum-from-serial-number 148 "B" 11) INFO:: Command: (seqnum-from-serial-number 148 "B" 12) INFO:: Command: (seqnum-from-serial-number 148 "B" 13) INFO:: Command: (seqnum-from-serial-number 148 "B" 14) INFO:: Command: (seqnum-from-serial-number 148 "B" 15) INFO:: Command: (seqnum-from-serial-number 148 "B" 16) INFO:: Command: (seqnum-from-serial-number 148 "B" 17) INFO:: Command: (seqnum-from-serial-number 148 "B" 18) INFO:: Command: (seqnum-from-serial-number 148 "B" 19) INFO:: Command: (seqnum-from-serial-number 148 "B" 20) INFO:: Command: (seqnum-from-serial-number 148 "B" 21) INFO:: Command: (seqnum-from-serial-number 148 "B" 22) INFO:: Command: (seqnum-from-serial-number 148 "B" 23) INFO:: Command: (seqnum-from-serial-number 148 "B" 24) INFO:: Command: (seqnum-from-serial-number 148 "B" 25) INFO:: Command: (seqnum-from-serial-number 148 "B" 26) INFO:: Command: (seqnum-from-serial-number 148 "B" 27) INFO:: Command: (seqnum-from-serial-number 148 "B" 28) INFO:: Command: (seqnum-from-serial-number 148 "B" 29) INFO:: Command: (seqnum-from-serial-number 148 "B" 30) INFO:: Command: (seqnum-from-serial-number 148 "B" 31) INFO:: Command: (seqnum-from-serial-number 148 "B" 32) INFO:: Command: (seqnum-from-serial-number 148 "B" 33) INFO:: Command: (seqnum-from-serial-number 148 "B" 34) INFO:: Command: (seqnum-from-serial-number 148 "B" 35) INFO:: Command: (seqnum-from-serial-number 148 "B" 36) INFO:: Command: (seqnum-from-serial-number 148 "B" 37) INFO:: Command: (seqnum-from-serial-number 148 "B" 38) INFO:: Command: (seqnum-from-serial-number 148 "B" 39) INFO:: Command: (seqnum-from-serial-number 148 "B" 40) INFO:: Command: (seqnum-from-serial-number 148 "B" 41) INFO:: Command: (seqnum-from-serial-number 148 "B" 42) INFO:: Command: (seqnum-from-serial-number 148 "B" 43) INFO:: Command: (seqnum-from-serial-number 148 "B" 44) INFO:: Command: (seqnum-from-serial-number 148 "B" 45) INFO:: Command: (seqnum-from-serial-number 148 "B" 46) INFO:: Command: (seqnum-from-serial-number 148 "B" 47) INFO:: Command: (seqnum-from-serial-number 148 "B" 48) INFO:: Command: (seqnum-from-serial-number 148 "B" 49) INFO:: Command: (seqnum-from-serial-number 148 "B" 50) INFO:: Command: (seqnum-from-serial-number 148 "B" 51) INFO:: Command: (seqnum-from-serial-number 148 "B" 52) INFO:: Command: (seqnum-from-serial-number 148 "B" 53) INFO:: Command: (seqnum-from-serial-number 148 "B" 54) INFO:: Command: (seqnum-from-serial-number 148 "B" 55) INFO:: Command: (seqnum-from-serial-number 148 "B" 56) INFO:: Command: (seqnum-from-serial-number 148 "B" 57) INFO:: Command: (seqnum-from-serial-number 148 "B" 58) INFO:: Command: (seqnum-from-serial-number 148 "B" 59) INFO:: Command: (seqnum-from-serial-number 148 "B" 60) INFO:: Command: (seqnum-from-serial-number 148 "B" 61) INFO:: Command: (seqnum-from-serial-number 148 "B" 62) INFO:: Command: (seqnum-from-serial-number 148 "B" 63) INFO:: Command: (seqnum-from-serial-number 148 "B" 64) INFO:: Command: (seqnum-from-serial-number 148 "B" 65) INFO:: Command: (seqnum-from-serial-number 148 "B" 66) INFO:: Command: (seqnum-from-serial-number 148 "B" 67) INFO:: Command: (seqnum-from-serial-number 148 "B" 68) INFO:: Command: (seqnum-from-serial-number 148 "B" 69) INFO:: Command: (seqnum-from-serial-number 148 "B" 70) INFO:: Command: (seqnum-from-serial-number 148 "B" 71) INFO:: Command: (seqnum-from-serial-number 148 "B" 72) INFO:: Command: (seqnum-from-serial-number 148 "B" 73) INFO:: Command: (seqnum-from-serial-number 148 "B" 74) INFO:: Command: (seqnum-from-serial-number 148 "B" 75) INFO:: Command: (seqnum-from-serial-number 148 "B" 76) INFO:: Command: (seqnum-from-serial-number 148 "B" 77) INFO:: Command: (seqnum-from-serial-number 148 "B" 78) INFO:: Command: (seqnum-from-serial-number 148 "B" 79) INFO:: Command: (seqnum-from-serial-number 148 "B" 80) INFO:: Command: (seqnum-from-serial-number 148 "B" 81) INFO:: Command: (seqnum-from-serial-number 148 "B" 82) INFO:: Command: (seqnum-from-serial-number 148 "B" 83) INFO:: Command: (seqnum-from-serial-number 148 "B" 84) INFO:: Command: (seqnum-from-serial-number 148 "B" 85) INFO:: Command: (seqnum-from-serial-number 148 "B" 86) INFO:: Command: (seqnum-from-serial-number 148 "B" 87) INFO:: Command: (seqnum-from-serial-number 148 "B" 88) INFO:: Command: (seqnum-from-serial-number 148 "B" 89) INFO:: Command: (seqnum-from-serial-number 148 "B" 90) INFO:: Command: (seqnum-from-serial-number 148 "B" 91) INFO:: Command: (seqnum-from-serial-number 148 "B" 92) INFO:: Command: (seqnum-from-serial-number 148 "B" 93) INFO:: Command: (seqnum-from-serial-number 148 "B" 94) INFO:: Command: (seqnum-from-serial-number 148 "B" 95) INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_4.pdb.gz INFO:: Command: (mutate 148 "A" 2 "" "TRP") DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 148 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 148 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_5.pdb.gz ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1t6q.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1t6q.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 149 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Wed_Aug__2_00:53:46_2017_modification_0.pdb.gz INFO:: Command: (mutate 149 "A" 50 "" "ASP") INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" INFO:: Command: (is-solvent-chain-p 149 "B") DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 149 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 149 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Wed_Aug__2_00:53:46_2017_modification_1.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Wed_Aug__2_00:53:46_2017_modification_2.pdb.gz result: [True, True] ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 150 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 150 and chain_id: B %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 1 Checking chains for NCS matching to chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 540 in second selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.4989 rms devi: 2.7962 max devi: 6.6860 min devi: 0.4401 find_ncs_matrix returns (LSQ) | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) Adding ghost with name: NCS found from matching Chain A onto Chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.6728 rms devi: 2.9369 max devi: 6.1200 min devi: 0.2483 find_ncs_matrix returns (LSQ) | -0.3504, -0.8022, -0.4834| | -0.7587, -0.05952, 0.6488| | -0.5492, 0.594, -0.5878| ( -29.05, 14.61, -72.53) Adding ghost with name: NCS found from matching Chain C onto Chain B INFO:: NCS chain comparison 61/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 1.7317 rms devi: 1.9769 max devi: 7.9453 min devi: 0.5297 find_ncs_matrix returns (LSQ) | -0.3815, -0.9208, -0.08098| | -0.9191, 0.3685, 0.1396| | -0.09874, 0.1277, -0.9869| ( -11.18, 4.757, -127.2) Adding ghost with name: NCS found from matching Chain D onto Chain B INFO:: NCS chain comparison 0/62 INFO:: set_ncs_master_chain Constructed 3 ghosts Ghost info:: NCS found from matching Chain A onto Chain B Ghost info:: NCS found from matching Chain C onto Chain B Ghost info:: NCS found from matching Chain D onto Chain B INFO:: Command: (copy-molecule 150) INFO:: Matching/moving molecule number 151 to 150 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Wed_Aug__2_00:54:02_2017_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) chain_id A master B rtop: [[0.3394591924816796, 0.5177117455596953, 0.7853292336015637, 0.8624279581117553, 0.16197572619124062, -0.4795642617960695, -0.3754803239943135, 0.8400823844328328, -0.39150493439900846], [90.55110034747929, -91.12318261711249, -47.52179998745863]] INFO:: Matching/moving molecule number 151 to 150 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.1943 rms devi: 0.2112 max devi: 0.3583 min devi: 0.0329 INFO:: Axis orientation: ( 0.1978, -0.3281, 0.9237) INFO:: Rotation in CCP4 Polar Angles: Polar = (22.5246,-58.9204,174.877) INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Wed_Aug__2_00:54:02_2017_modification_1.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | -0.9179, -0.212, 0.3353| | -0.04702, -0.7812, -0.6226| | 0.3939, -0.5873, 0.7071| ( 57.6, -116.4, -53.95) INFO:: fractional coordinates matrix: | -0.9451, -0.1016, -0.03159| | -0.05429, -0.754, -0.9411| | 0.3009, -0.5389, 0.7071| ( -0.109, -1.522, -0.4666) chain_id C master B rtop: [[-0.9179458350933407, -0.21199297393104302, 0.33531242571467806, -0.04701514428682865, -0.7811500284294697, -0.6225706460252742, 0.39390991361284383, -0.5872508936464131, 0.7070865349227144], [57.59590387868751, -116.43599115338534, -53.953192756327674]] INFO:: Matching/moving molecule number 151 to 150 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.4174 rms devi: 0.4531 max devi: 0.7926 min devi: 0.0759 INFO:: Axis orientation: ( 0.7055, 0.6938, 0.1447) INFO:: Rotation in CCP4 Polar Angles: Polar = (98.3189,-135.478,101.097) INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Wed_Aug__2_00:54:02_2017_modification_2.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.401, 0.7256, -0.5591| | 0.4417, 0.3815, 0.812| | 0.8025, -0.5726, -0.1675| ( 8.426, 15.74, -123.4) INFO:: fractional coordinates matrix: | 0.656, 0.4912, -0.1182| | 0.51, 0.1265, 1.227| | 0.6131, -0.6853, -0.1675| ( 0.1983, 0.2058, -1.067) chain_id D master B rtop: [[0.4010296958260637, 0.7256475124974693, -0.5591161513244722, 0.44169126456601965, 0.38154476969746226, 0.8119928666697639, 0.8025484470558306, -0.5725899722513011, -0.16750138448839502], [8.42628578842055, 15.739925910905619, -123.41057067974724]] INFO:: Command: (close-molecule 151) NCS ghost chain IDs pre: [['B', 'A', 'C', 'D']] NCS ghost chain IDs post: [['B', 'A', 'C', 'D']] ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... INFO:: Command: (molecule-name 0) INFO:: Command: (molecule-name 1) INFO:: Command: (molecule-name 4) INFO:: Command: (molecule-name 5) INFO:: Command: (molecule-name 6) INFO:: Command: (molecule-name 7) INFO:: Command: (molecule-name 8) INFO:: Command: (molecule-name 9) INFO:: Command: (molecule-name 10) INFO:: Command: (molecule-name 11) INFO:: Command: (molecule-name 13) INFO:: Command: (molecule-name 14) INFO:: Command: (molecule-name 15) INFO:: Command: (molecule-name 17) INFO:: Command: (molecule-name 18) INFO:: Command: (molecule-name 21) INFO:: Command: (molecule-name 22) INFO:: Command: (molecule-name 23) INFO:: Command: (molecule-name 25) INFO:: Command: (molecule-name 26) INFO:: Command: (molecule-name 28) INFO:: Command: (molecule-name 29) INFO:: Command: (molecule-name 30) INFO:: Command: (molecule-name 32) INFO:: Command: (molecule-name 33) INFO:: Command: (molecule-name 34) INFO:: Command: (molecule-name 35) INFO:: Command: (molecule-name 36) INFO:: Command: (molecule-name 39) INFO:: Command: (molecule-name 48) INFO:: Command: (molecule-name 50) INFO:: Command: (molecule-name 51) INFO:: Command: (molecule-name 52) INFO:: Command: (molecule-name 53) INFO:: Command: (molecule-name 54) INFO:: Command: (molecule-name 55) INFO:: Command: (molecule-name 56) INFO:: Command: (molecule-name 57) INFO:: Command: (molecule-name 58) INFO:: Command: (molecule-name 59) INFO:: Command: (molecule-name 60) INFO:: Command: (molecule-name 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 64) INFO:: Command: (molecule-name 65) INFO:: Command: (molecule-name 66) INFO:: Command: (molecule-name 67) INFO:: Command: (molecule-name 68) INFO:: Command: (molecule-name 69) INFO:: Command: (molecule-name 70) INFO:: Command: (molecule-name 71) INFO:: Command: (molecule-name 72) INFO:: Command: (molecule-name 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 76) INFO:: Command: (molecule-name 77) INFO:: Command: (molecule-name 78) INFO:: Command: (molecule-name 79) INFO:: Command: (molecule-name 80) INFO:: Command: (molecule-name 81) INFO:: Command: (molecule-name 82) INFO:: Command: (molecule-name 83) INFO:: Command: (molecule-name 84) INFO:: Command: (molecule-name 85) INFO:: Command: (molecule-name 86) INFO:: Command: (molecule-name 87) INFO:: Command: (molecule-name 88) INFO:: Command: (molecule-name 89) INFO:: Command: (molecule-name 90) INFO:: Command: (molecule-name 92) INFO:: Command: (molecule-name 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 98) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 101) INFO:: Command: (molecule-name 102) INFO:: Command: (molecule-name 103) INFO:: Command: (molecule-name 104) INFO:: Command: (molecule-name 105) INFO:: Command: (molecule-name 106) INFO:: Command: (molecule-name 107) INFO:: Command: (molecule-name 108) INFO:: Command: (molecule-name 109) INFO:: Command: (molecule-name 110) INFO:: Command: (molecule-name 111) INFO:: Command: (molecule-name 112) INFO:: Command: (molecule-name 113) INFO:: Command: (molecule-name 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 119) INFO:: Command: (molecule-name 120) INFO:: Command: (molecule-name 121) INFO:: Command: (molecule-name 122) INFO:: Command: (molecule-name 123) INFO:: Command: (molecule-name 124) INFO:: Command: (molecule-name 125) INFO:: Command: (molecule-name 126) INFO:: Command: (molecule-name 127) INFO:: Command: (molecule-name 128) INFO:: Command: (molecule-name 129) INFO:: Command: (molecule-name 130) INFO:: Command: (molecule-name 131) INFO:: Command: (molecule-name 132) INFO:: Command: (molecule-name 133) INFO:: Command: (molecule-name 135) INFO:: Command: (molecule-name 136) INFO:: Command: (molecule-name 137) INFO:: Command: (molecule-name 138) INFO:: Command: (molecule-name 139) INFO:: Command: (molecule-name 140) INFO:: Command: (molecule-name 141) INFO:: Command: (close-molecule 143) INFO:: Command: (close-molecule 145) INFO:: Command: (molecule-name 147) INFO:: Command: (molecule-name 148) INFO:: Command: (molecule-name 149) INFO:: Command: (molecule-name 150) INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 1) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 152 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /lmb/home/pemsley/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:: 0.0320 seconds to read MTZ file INFO:: 0.0190 seconds to initialize map INFO:: 0.0210 seconds for FFT INFO:: Map statistics: mean: -0.0000 st.d: 0.2241 INFO:: Map statistics: min: -0.8818 max: 1.7219 INFO:: 0.0050 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0230 seconds for contour map INFO:: 0.1000 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 153 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 153 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) INFO:: Map statistics: mean: -0.0008 st.d: 0.1767 INFO:: Map statistics: min: -0.9977 max: 1.4866 Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5946 0.3997 3628 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 153 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 153 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) INFO:: Map statistics: mean: -0.0008 st.d: 0.1767 INFO:: Map statistics: min: -0.9977 max: 1.4866 Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5946 0.3997 3628 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 153 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 153 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) INFO:: Map statistics: mean: -0.0008 st.d: 0.1767 INFO:: Map statistics: min: -0.9977 max: 1.4866 Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5946 0.3997 3628 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: Command: (molecule-name 0) INFO:: Command: (molecule-name 1) INFO:: Command: (molecule-name 4) INFO:: Command: (molecule-name 5) INFO:: Command: (molecule-name 6) INFO:: Command: (molecule-name 7) INFO:: Command: (molecule-name 8) INFO:: Command: (molecule-name 9) INFO:: Command: (molecule-name 10) INFO:: Command: (molecule-name 11) INFO:: Command: (molecule-name 13) INFO:: Command: (molecule-name 14) INFO:: Command: (molecule-name 15) INFO:: Command: (molecule-name 17) INFO:: Command: (molecule-name 18) INFO:: Command: (molecule-name 21) INFO:: Command: (molecule-name 22) INFO:: Command: (molecule-name 23) INFO:: Command: (molecule-name 25) INFO:: Command: (molecule-name 26) INFO:: Command: (molecule-name 28) INFO:: Command: (molecule-name 29) INFO:: Command: (molecule-name 30) INFO:: Command: (molecule-name 32) INFO:: Command: (molecule-name 33) INFO:: Command: (molecule-name 34) INFO:: Command: (molecule-name 35) INFO:: Command: (molecule-name 36) INFO:: Command: (molecule-name 39) INFO:: Command: (molecule-name 48) INFO:: Command: (molecule-name 50) INFO:: Command: (molecule-name 51) INFO:: Command: (molecule-name 52) INFO:: Command: (molecule-name 53) INFO:: Command: (molecule-name 54) INFO:: Command: (molecule-name 55) INFO:: Command: (molecule-name 56) INFO:: Command: (molecule-name 57) INFO:: Command: (molecule-name 58) INFO:: Command: (molecule-name 59) INFO:: Command: (molecule-name 60) INFO:: Command: (molecule-name 61) INFO:: Command: (molecule-name 62) INFO:: Command: (molecule-name 64) INFO:: Command: (molecule-name 65) INFO:: Command: (molecule-name 66) INFO:: Command: (molecule-name 67) INFO:: Command: (molecule-name 68) INFO:: Command: (molecule-name 69) INFO:: Command: (molecule-name 70) INFO:: Command: (molecule-name 71) INFO:: Command: (molecule-name 72) INFO:: Command: (molecule-name 73) INFO:: Command: (molecule-name 74) INFO:: Command: (molecule-name 76) INFO:: Command: (molecule-name 77) INFO:: Command: (molecule-name 78) INFO:: Command: (molecule-name 79) INFO:: Command: (molecule-name 80) INFO:: Command: (molecule-name 81) INFO:: Command: (molecule-name 82) INFO:: Command: (molecule-name 83) INFO:: Command: (molecule-name 84) INFO:: Command: (molecule-name 85) INFO:: Command: (molecule-name 86) INFO:: Command: (molecule-name 87) INFO:: Command: (molecule-name 88) INFO:: Command: (molecule-name 89) INFO:: Command: (molecule-name 90) INFO:: Command: (molecule-name 92) INFO:: Command: (molecule-name 93) INFO:: Command: (molecule-name 94) INFO:: Command: (molecule-name 98) INFO:: Command: (molecule-name 99) INFO:: Command: (molecule-name 101) INFO:: Command: (molecule-name 102) INFO:: Command: (molecule-name 103) INFO:: Command: (molecule-name 104) INFO:: Command: (molecule-name 105) INFO:: Command: (molecule-name 106) INFO:: Command: (molecule-name 107) INFO:: Command: (molecule-name 108) INFO:: Command: (molecule-name 109) INFO:: Command: (molecule-name 110) INFO:: Command: (molecule-name 111) INFO:: Command: (molecule-name 112) INFO:: Command: (molecule-name 113) INFO:: Command: (molecule-name 114) INFO:: Command: (molecule-name 115) INFO:: Command: (molecule-name 119) INFO:: Command: (molecule-name 120) INFO:: Command: (molecule-name 121) INFO:: Command: (molecule-name 122) INFO:: Command: (molecule-name 123) INFO:: Command: (molecule-name 124) INFO:: Command: (molecule-name 125) INFO:: Command: (molecule-name 126) INFO:: Command: (molecule-name 127) INFO:: Command: (molecule-name 128) INFO:: Command: (molecule-name 129) INFO:: Command: (molecule-name 130) INFO:: Command: (molecule-name 131) INFO:: Command: (molecule-name 132) INFO:: Command: (molecule-name 133) INFO:: Command: (molecule-name 135) INFO:: Command: (molecule-name 136) INFO:: Command: (molecule-name 137) INFO:: Command: (molecule-name 138) INFO:: Command: (molecule-name 139) INFO:: Command: (molecule-name 140) INFO:: Command: (molecule-name 141) INFO:: Command: (molecule-name 147) INFO:: Command: (molecule-name 148) INFO:: Command: (molecule-name 149) INFO:: Command: (molecule-name 150) INFO:: Command: (molecule-name 152) BL DEBUG:: molecule_names ['/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'mainchain', '/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb', 'regression-test-terminal-residue.pdb', 'atom selection from regression-test-terminal-residue.pdb', '/lmb/home/pemsley/data/greg-data/frag-2wot.pdb', 'sphere selection from tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb', '/lmb/home/pemsley/data/greg-data/res098.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/pdb3knw.ent', '/lmb/home/pemsley/data/greg-data/pdb1py3.ent', '/lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb', '/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT', '/lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb', '/lmb/home/pemsley/data/greg-data/val.pdb', '/lmb/home/pemsley/data/greg-data/2yie-frag.pdb', '/lmb/home/pemsley/data/greg-data/4f8g.pdb', '/lmb/home/pemsley/data/greg-data/4f8g.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'Generic Masked Map', 'difference-map', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'averaged-map', 'difference-map', '/lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/monomer-VAL.pdb', '/lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb', 'atom selection from tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'atom selection from tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb3hfl.ent', '/lmb/home/pemsley/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_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb', '/lmb/home/pemsley/data/greg-data/tm+some-waters.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb', '/lmb/home/pemsley/data/greg-data/pathological-water-test.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb1hvv.ent', '/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb', '/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'SymOp_-X,-X+Y,-Z+1/3_Copy_of_78', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb1py3.ent', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/2goz-manip.pdb', 'rnase_zip_test.pdb.gz', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/HOF.RES', '/lmb/home/pemsley/data/greg-data/hollander.ins', '/lmb/home/pemsley/data/greg-data/insulin.fcf Diff-SigmaA', 'atom selection from insulin.res', 'atom selection from insulin.res', '/lmb/home/pemsley/data/greg-data/horma-p21.res', 'new-horma.ins', '/lmb/home/pemsley/data/greg-data/crash.hat', '/lmb/home/pemsley/data/greg-data/crash.hat', 'coot-ccp4/monomer-3GP.pdb', '/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb', '/lmb/home/pemsley/data/greg-data/test-LIG.pdb', '/lmb/home/pemsley/data/greg-data/test-LIG.pdb', '/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', '/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb', '/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT', 'Masked (by protein)', 'Fitted ligand #0-0', 'Fitted ligand #1-0', 'Fitted ligand #2-0', 'Fitted ligand #3-0', 'Fitted ligand #4-0', 'Fitted ligand #5-0', 'Fitted ligand #6-0', 'Fitted ligand #7-0', 'Fitted ligand #8-0', 'Fitted ligand #9-0', 'coot-ccp4/monomer-3GP.pdb', 'Copy_of_coot-ccp4/monomer-3GP.pdb', '/lmb/home/pemsley/data/greg-data/dipole-residues.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb', '/lmb/home/pemsley/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', '/lmb/home/pemsley/data/greg-data/1wly.pdb', '/lmb/home/pemsley/data/greg-data/1yb5.pdb', '/lmb/home/pemsley/data/greg-data/2qd9.pdb', '/lmb/home/pemsley/data/greg-data/2gtn.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Map 2 NCS average of Chain A type molecules', 'Map 142 NCS average of Chain A type molecules', '/lmb/home/pemsley/data/greg-data/insulin.res', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb1t6q.ent', '/lmb/home/pemsley/data/greg-data/pdb1hvv.ent', '/lmb/home/pemsley/data/greg-data/pdb1hvv.ent', '/lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Map 153 NCS found from matching Chain B onto Chain A', 'Map 153 NCS found from matching Chain C onto Chain A', 'Map 153 NCS found from matching Chain D onto Chain A', 'Map 153 NCS average of Chain A type molecules', 'Map 153 NCS found from matching Chain B onto Chain A', 'Map 153 NCS found from matching Chain C onto Chain A', 'Map 153 NCS found from matching Chain D onto Chain A', 'Map 153 NCS average of Chain A type molecules'] BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 BL DEBUG:: n_matchers 2 ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... INFO:: Command: (+ 2 4) INFO:: Command: (rotation-centre) INFO:: Command: (rotation-centre-position 0) INFO:: Command: (rotation-centre-position 1) INFO:: Command: (rotation-centre-position 2) BL DEBUG:: return scheme is [24.219083786010742, -41.04264831542969, -67.95923614501953] INFO:: Command: 2 ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... Entering test: kevin's torsion test PASS: kevin's torsion test Entering test: test_alt_conf_rotamers INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_alt_conf_rotamers Entering test: test_fragmemt_atom_selection INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 n_initial: 1465 n_1: 1401 n_2: 64 PASS: test_fragmemt_atom_selection Entering test: test_add_atom INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 PASS: test_add_atom Entering test: test dictionary partial charges INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif PASS: test dictionary partial charges Entering test: test segid exchange INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Test with a rogue segid INFO:: No consistent segids for residue 1 PASS: test segid exchange Entering test: test ligand from point There are 2 data in /lmb/home/pemsley/data/greg-data/libcheck_3GP-torsion-filtered.cif INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... non-H torsion: 0 [torsion-restraint: CONST_1 O6 C6 C5 N7 0.0000 0.0000 0 CONST ] non-H torsion: 1 [torsion-restraint: CONST_2 C6 C5 C4 N3 0.0000 0.0000 0 CONST ] non-H torsion: 2 [torsion-restraint: CONST_3 C6 C5 C4 N9 180.0000 0.0000 0 CONST ] non-H torsion: 3 [torsion-restraint: CONST_4 C5 C4 N3 C2 0.0000 0.0000 0 CONST ] non-H torsion: 4 [torsion-restraint: CONST_5 C4 N3 C2 N1 0.0000 0.0000 0 CONST ] non-H torsion: 5 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] non-H torsion: 6 [torsion-restraint: CONST_6 N3 C2 N1 C6 0.0000 0.0000 0 CONST ] non-H torsion: 7 [torsion-restraint: CONST_12 N3 C2 N1 HN1 180.0000 0.0000 0 CONST ] non-H torsion: 8 [torsion-restraint: CONST_7 C6 C5 N7 C8 180.0000 0.0000 0 CONST ] non-H torsion: 9 [torsion-restraint: CONST_8 C5 N7 C8 N9 0.0000 0.0000 0 CONST ] non-H torsion: 10 [torsion-restraint: CONST_9 N7 C8 N9 C1* 180.0000 0.0000 0 CONST ] non-H torsion: 11 [torsion-restraint: CONST_10 N7 C8 N9 C4 0.0000 0.0000 0 CONST ] non-H torsion: 12 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] non-H torsion: 13 [torsion-restraint: CONST_var_3 N9 C1* O4* C4* -152.9040 20.0000 1 CONST ] non-H torsion: 14 [torsion-restraint: CONST_var_4 C1* O4* C4* C5* 124.2120 20.0000 1 CONST ] non-H torsion: 15 [torsion-restraint: CONST_var_5 C1* O4* C4* C3* -3.5110 20.0000 1 CONST ] non-H torsion: 16 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] non-H torsion: 17 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] non-H torsion: 18 [torsion-restraint: CONST_var_8 N9 C1* C2* C3* 155.4840 20.0000 3 CONST ] non-H torsion: 19 [torsion-restraint: CONST_var_9 C1* C2* O2* HO2* 0.0000 20.0000 1 CONST ] non-H torsion: 20 [torsion-restraint: CONST_var_10 C1* C2* C3* O3* 82.0740 20.0000 3 CONST ] non-H torsion: 21 [torsion-restraint: CONST_11 C1* C2* C3* H3* -157.9260 0.0000 0 CONST ] non-H torsion: 22 [torsion-restraint: CONST_var_11 C1* C2* C3* C4* -36.8410 20.0000 3 CONST ] non-H torsion: 23 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] non-H torsion: 24 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] non-H-non-ring-non-const torsion: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] non-H-non-ring-non-const torsion: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] non-H-non-ring-non-const torsion: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] non-H-non-ring-non-const torsion: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] non-H-non-ring-non-const torsion: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] non-H-non-ring-non-const torsion: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 14.7762 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -54.9516 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] 162.6106 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] 8.4938 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -195.4683 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -166.4554 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 377 non-bonded restraints initial distortion_score: 24.1438 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0314 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 332) at 10.8808 Final Estimated RMS Z Scores: bonds: 0.0855 angles: 0.3991 torsions: N/A planes: 0.0184 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 36.4975 76.1647 445.5317 ligand eigen vectors: | -0.07977, 0.2304, -0.9698| | -0.4027, 0.8825, 0.2428| | 0.9119, 0.4099, 0.02239| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 37.0743 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -49.1207 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] 187.9187 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] -11.1421 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -178.1636 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -169.0043 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 380 non-bonded restraints initial distortion_score: 165.2660 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.4025 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 359) at 11.0005 Final Estimated RMS Z Scores: bonds: 0.0834 angles: 0.4015 torsions: N/A planes: 0.0301 non-bonded: 0.0003 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 40.4491 75.2040 439.3141 ligand eigen vectors: | -0.01617, 0.2434, -0.9698| | -0.3291, 0.9146, 0.235| | 0.9442, 0.323, 0.06531| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 12.1869 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -89.8476 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] 152.9450 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] -10.1671 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -220.6830 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -138.9559 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 381 non-bonded restraints initial distortion_score: 22.6852 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0273 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 317) at 10.8449 Final Estimated RMS Z Scores: bonds: 0.0842 angles: 0.3986 torsions: N/A planes: 0.0357 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 24.7987 97.9331 424.9583 ligand eigen vectors: | -0.1827, 0.1536, -0.9711| | -0.2572, 0.9459, 0.198| | 0.9489, 0.2859, -0.1333| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 22.9319 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -81.4598 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] 191.6705 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] -28.0568 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -170.5559 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -164.7228 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 379 non-bonded restraints initial distortion_score: 88.7771 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.2018 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 499) at 11.0813 Final Estimated RMS Z Scores: bonds: 0.0850 angles: 0.4029 torsions: N/A planes: 0.0042 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A ligand eigen values: 23.5873 88.9388 439.7719 ligand eigen vectors: | -0.09012, 0.2069, -0.9742| | -0.1806, 0.9586, 0.2203| | 0.9794, 0.1958, -0.04902| non-const-non-ring-tors: 0 [torsion-restraint: var_1 N3 C2 N2 HN21 0.0000 20.0000 1] 1.5000 non-const-non-ring-tors: 1 [torsion-restraint: var_2 C8 N9 C1* C2* -78.3750 20.0000 1] -90.1820 non-const-non-ring-tors: 2 [torsion-restraint: var_6 O4* C4* C5* O5* -61.6860 20.0000 3] 167.9219 non-const-non-ring-tors: 3 [torsion-restraint: var_7 C4* C5* O5* HO5* 0.0000 20.0000 1] -20.0368 non-const-non-ring-tors: 4 [torsion-restraint: var_12 C2* C3* O3* P -179.7030 20.0000 1] -171.9200 non-const-non-ring-tors: 5 [torsion-restraint: var_13 C3* O3* P O2P -156.9910 20.0000 1] -156.0362 created 38 bond restraints created 66 angle restraints created 1 plane restraints created 0 chiral vol restraints created 105 restraints INFO:: make_restraints(): made 378 non-bonded restraints initial distortion_score: 36.6299 Initial RMS Z values bonds: 0.1236 angles: 0.4213 torsions: N/A planes: 0.0586 non-bonded: 0.0644 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 527) at 11.1991 Final Estimated RMS Z Scores: bonds: 0.0845 angles: 0.4053 torsions: N/A planes: 0.0102 non-bonded: 0.0002 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A INFO:: Protein centre at: xyz = ( 41.53, 8.726, 12.87) There are 1 clusters Here are the top 10 clusters: Number: 0 # grid points: 264 score: 146.5952 | -0.1765, 0.981, -0.08001| | 0.2847, 0.1287, 0.9499| | 0.9422, 0.1449, -0.302| ( 55.49, 9.316, 20.62) xyz = ( 3.05, 1.281, 0.8881) eigenvalues: 131.0082 2545.3515 421.9402 found distance from reference centre 0.2766 PASS: test ligand from point Entering test: test peak search non-close reading mtz file... Number of reflections: 17982 finding ASU unique map points... Grid...Nuvw = ( 108, 132, 64) doing fft... done fft... INFO:: peak filtering: npeaks: in: 5158 out: 2105 There are 2105 peaks and 0 problem peaks PASS: test peak search non-close Entering test: test symop card 1 0 0 0 1 0 0 0 1 translations: -1.0000 0.0000 0.0000 PASS: test symop card Entering test: test rotate round vector INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read. Spacegroup: P 1 0 O6 0.9397 -> 20.0000 degrees 1 C6 0.9397 -> 20.0000 degrees 2 C5 0.9397 -> 20.0000 degrees 3 C4 0.9397 -> 20.0000 degrees 4 N3 0.9397 -> 20.0000 degrees 5 C2 0.9397 -> 20.0000 degrees 6 N2 0.9397 -> 20.0000 degrees 7 HN22 0.9397 -> 20.0000 degrees 8 HN21 0.9397 -> 20.0000 degrees 9 N1 0.9397 -> 20.0000 degrees 10 HN1 0.9397 -> 20.0000 degrees 11 N7 0.9397 -> 20.0000 degrees 12 C8 0.9397 -> 20.0000 degrees 13 H8 0.9397 -> 20.0000 degrees 16 H1* 0.9397 -> 20.0000 degrees 17 O4* 0.9397 -> 20.0000 degrees 18 C4* 0.9397 -> 20.0000 degrees 19 H4* 0.9397 -> 20.0000 degrees 20 C5* 0.9397 -> 20.0000 degrees 21 H5*1 0.9397 -> 20.0000 degrees 22 H5*2 0.9397 -> 20.0000 degrees 23 O5* 0.9397 -> 20.0000 degrees 24 HO5* 0.9397 -> 20.0000 degrees 25 C2* 0.9397 -> 20.0000 degrees 26 H2* 0.9397 -> 20.0000 degrees 27 O2* 0.9397 -> 20.0000 degrees 28 HO2* 0.9397 -> 20.0000 degrees 29 C3* 0.9397 -> 20.0000 degrees 30 H3* 0.9397 -> 20.0000 degrees 31 O3* 0.9397 -> 20.0000 degrees 32 P 0.9397 -> 20.0000 degrees 33 O1P 0.9397 -> 20.0000 degrees 34 O3P 0.9397 -> 20.0000 degrees 35 O2P 0.9397 -> 20.0000 degrees PASS: test rotate round vector Entering test: SSM sequence alignment output -- Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC -- Moving: D Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG -- Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG -- PASS: SSM sequence alignment output ok ---------------------------------------------------------------------- Ran 125 tests in 276.260s OK test00_0 (__main__.PdbMtzTestFunctions) Post Go To Atom no molecule ... ok test01_0 (__main__.PdbMtzTestFunctions) Close bad molecule ... ok test02_0 (__main__.PdbMtzTestFunctions) Read coordinates test ... ok test03_0 (__main__.PdbMtzTestFunctions) New molecule from bogus molecule ... ok test03_1 (__main__.PdbMtzTestFunctions) Don't crash on empty NCS from mmCIF file ... ok test04_0 (__main__.PdbMtzTestFunctions) New molecule from bogus atom selection ... ok test05_0 (__main__.PdbMtzTestFunctions) ins code change and Goto atom over an ins code break ... ok test06_0 (__main__.PdbMtzTestFunctions) Read a bogus map ... ok test07_0 (__main__.PdbMtzTestFunctions) Read MTZ test ... ok test07_1 (__main__.PdbMtzTestFunctions) Auto-read bad MTZ test ... ok test08_0 (__main__.PdbMtzTestFunctions) Map Sigma ... ok test09_0 (__main__.PdbMtzTestFunctions) Another Level Test ... ok test09_1 (__main__.PdbMtzTestFunctions) db-main makes mainchain ... ok test10_0 (__main__.PdbMtzTestFunctions) Set Atom Atribute Test ... ok test11_0 (__main__.PdbMtzTestFunctions) Add Terminal Residue Test ... ok test11_1 (__main__.PdbMtzTestFunctions) Adding residue by phi psi, no crash ... ok test12_0 (__main__.PdbMtzTestFunctions) Select by Sphere ... ok test13_0 (__main__.PdbMtzTestFunctions) Test Views ... ok test13_1 (__main__.PdbMtzTestFunctions) Delete Residue ... ok test14_0 (__main__.PdbMtzTestFunctions) Label Atoms and Delete ... ok test15_0 (__main__.PdbMtzTestFunctions) Rotamer outliers ... ok test16_0 (__main__.PdbMtzTestFunctions) Alt Conf Occ Sum Reset ... ok test16_1 (__main__.PdbMtzTestFunctions) Correct occupancies after auto-fit rotamer on alt-confed residue ... ok test16_2 (__main__.PdbMtzTestFunctions) Rotamers work on MSE ... ok test16_3 (__main__.PdbMtzTestFunctions) Hs are correctly swapped on a TYR ... ok test16_4 (__main__.PdbMtzTestFunctions) Splitting residue leaves no atoms with negative occupancy ... ok test17_0 (__main__.PdbMtzTestFunctions) Pepflip flips the correct alt confed atoms ... ok test18_0 (__main__.PdbMtzTestFunctions) Correction of CISPEP test ... ok test19_0 (__main__.PdbMtzTestFunctions) Refine Zone with Alt conf ... ok test20_0 (__main__.PdbMtzTestFunctions) Sphere Refine ... ok test20_1 (__main__.PdbMtzTestFunctions) Refinement gives useful results ... ok test21_0 (__main__.PdbMtzTestFunctions) Rigid Body Refine Alt Conf Waters ... ok test22_0 (__main__.PdbMtzTestFunctions) Setting multiple atom attributes ... ok test23_0 (__main__.PdbMtzTestFunctions) Tweak Alt Confs on Active Residue ... ok test24_0 (__main__.PdbMtzTestFunctions) Backrub rotamer ... ok test25_0 (__main__.PdbMtzTestFunctions) Libcif horne ... ok test26_0 (__main__.PdbMtzTestFunctions) Refmac Parameters Storage ... ok test26_1 (__main__.PdbMtzTestFunctions) OXT is added before TER record - add only one ... ok test27_0 (__main__.PdbMtzTestFunctions) The position of the oxygen after a mutation ... ok test27_1 (__main__.PdbMtzTestFunctions) TER is at the end of a nucleotide after mutation ... ok test27_2 (__main__.PdbMtzTestFunctions) C7 is removed on mutation from a DC ... ok test27_3 (__main__.PdbMtzTestFunctions) C7 is added on mutation to a DC ... ok test28_0 (__main__.PdbMtzTestFunctions) Deleting (non-existing) Alt conf and Go To Atom [JED] ... ok test29_0 (__main__.PdbMtzTestFunctions) Mask and difference map ... ok test29_1 (__main__.PdbMtzTestFunctions) Skeletonize a map ... ok test29_2 (__main__.PdbMtzTestFunctions) Simple Averaged maps ... ok test30_0 (__main__.PdbMtzTestFunctions) Make a glycosidic linkage ... ok test30_1 (__main__.PdbMtzTestFunctions) Refine an NAG-ASN Link ... ok test31_0 (__main__.PdbMtzTestFunctions) Test for flying hydrogens on undo ... ok test32_0 (__main__.PdbMtzTestFunctions) Test for mangling of hydrogen names from a PDB v 3.0 ... ok test32_1 (__main__.PdbMtzTestFunctions) Correct matching dictionary names from test name ... ok test33_0 (__main__.PdbMtzTestFunctions) Update monomer restraints ... ok test33_1 (__main__.PdbMtzTestFunctions) Write mmCIF restraints correctly ... ok test34_0 (__main__.PdbMtzTestFunctions) Refinement OK with zero bond esd ... ok test35_0 (__main__.PdbMtzTestFunctions) Change Chain IDs and Chain Sorting ... ok test36_0 (__main__.PdbMtzTestFunctions) Replace Fragment ... ok test37_0 (__main__.PdbMtzTestFunctions) Residues in Region of Residue ... ok test38_0 (__main__.PdbMtzTestFunctions) Residues in region of a point ... ok test39_0 (__main__.PdbMtzTestFunctions) Empty molecule on type selection ... ok test40_0 (__main__.PdbMtzTestFunctions) Set Rotamer ... ok test41_0 (__main__.PdbMtzTestFunctions) Rotamer names and scores are correct ... ok test42_0 (__main__.PdbMtzTestFunctions) Align and mutate a model with deletions ... ok test42_1 (__main__.PdbMtzTestFunctions) Renumber residues should be in seqnum order ... ok test43_0 (__main__.PdbMtzTestFunctions) Autofit Rotamer on Residue with Insertion codes ... ok test44_0 (__main__.PdbMtzTestFunctions) RNA base has correct residue type after mutation ... ok test45_0 (__main__.PdbMtzTestFunctions) DNA bases are the correct residue type after mutation ... ok test46_0 (__main__.PdbMtzTestFunctions) SegIDs are correct after mutate ... ok test47_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding a water by hand ... ok test48_0 (__main__.PdbMtzTestFunctions) TER on water chain is removed on adding waters automatically ... ok test48_1 (__main__.PdbMtzTestFunctions) Adding atoms to Many-Chained Molecule ... ok test49_0 (__main__.PdbMtzTestFunctions) Arrange waters round protein ... ok test50_0 (__main__.PdbMtzTestFunctions) Correct Segid After Add Terminal Residue ... ok test51_0 (__main__.PdbMtzTestFunctions) Correct Segid after NCS residue range copy ... ok test52_0 (__main__.PdbMtzTestFunctions) Merge Water Chains ... ok test52_1 (__main__.PdbMtzTestFunctions) Consolidated merge ... ok test53_0 (__main__.PdbMtzTestFunctions) LSQ by atom ... ok test53_1 (__main__.PdbMtzTestFunctions) LSQing changes the space-group and cell to that of the reference molecule ... ok test53_2 (__main__.PdbMtzTestFunctions) set_residue_name sets the correct residue ... ok test53_3 (__main__.PdbMtzTestFunctions) fit_protein_make_specs makes all specs ... ok test54_0 (__main__.PdbMtzTestFunctions) Phosphate distance in pucker analysis is sane ... ok test60_0 (__main__.PdbMtzTestFunctions) post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok test61_0 (__main__.PdbMtzTestFunctions) Read/write gz coordinate files ... ok test62_0 (__main__.PdbMtzTestFunctions) Fix for Oliver Clarke fit by atom selection bug ... ok test999_0 (__main__.PdbMtzTestFunctions) Renumber residue range without overwriting coordinates. ... ok test01_0 (__main__.ShelxTestFunctions) Read small molecule .res file ... ok test02_0 (__main__.ShelxTestFunctions) Read hollander small molecule .res file ... ok test03_0 (__main__.ShelxTestFunctions) read shelx insulin with fcf ... ok test04_0 (__main__.ShelxTestFunctions) Write an INS from PDB test ... ok test05_0 (__main__.ShelxTestFunctions) new molecule by atom selection inherits shelx molecule flag ... ok test06_0 (__main__.ShelxTestFunctions) Addition of Terminal Residue on SHELX molecule has correct occupancy ... ok test07_0 (__main__.ShelxTestFunctions) Add water to SHELX molecule ... ok test08_0 (__main__.ShelxTestFunctions) Find Waters for a SHELXL molecule ... ok test09_0 (__main__.ShelxTestFunctions) NPD Anisotropic Atom [Mitch Miller] ... ok test10_0 (__main__.ShelxTestFunctions) close shelx molecules ... ok test11_0 (__main__.ShelxTestFunctions) Aniso Bs in P21 ... ok test12_0 (__main__.ShelxTestFunctions) Don't crash on reading a strange HAT file ... ok test01_0 (__main__.LigandTestFunctions) Get monomer test ... ok test02_0 (__main__.LigandTestFunctions) Set Bond thickness test ... ok test03_0 (__main__.LigandTestFunctions) Delete all-molecule Hydrogens ... ok test04_0 (__main__.LigandTestFunctions) Non-Autoloads ... ok test05_0 (__main__.LigandTestFunctions) Move and Refine Ligand test ... ok test06_0 (__main__.LigandTestFunctions) Many Molecules - Ligand Fitting ... ok test07_0 (__main__.LigandTestFunctions) Flip residue (around eigen vectors) ... ok test08_0 (__main__.LigandTestFunctions) Test dipole ... ok test09_0 (__main__.LigandTestFunctions) Reading new dictionary restraints replaces ... ok test10_0 (__main__.LigandTestFunctions) Pyrogen Runs OK? ... ok test11_0 (__main__.LigandTestFunctions) pyrogen dictionary does not make double-quoted atom names ... ok test01_0 (__main__.CootaneerTestFunctions) Assignment of new PIR sequence overwrites old assignment ... ok test02_0 (__main__.CootaneerTestFunctions) Cootaneer Beta Strand ... ok test01_0 (__main__.RnaGhostsTestFunctions) RNA NCS Ghosts ... ok test01_0 (__main__.SsmTestFunctions) SSM - Frank von Delft's Example ... ok test02_0 (__main__.SsmTestFunctions) SSM - Alice Dawson's Example ... ok test03_0 (__main__.SsmTestFunctions) SSM by atom selection [JED Example] ... ok test01_1 (__main__.NcsTestFunctions) NCS maps test ... ok test02_0 (__main__.NcsTestFunctions) NCS chains info ... ok test03_0 (__main__.NcsTestFunctions) NCS deviation info ... ok test04_0 (__main__.NcsTestFunctions) NCS Residue Range copy ... ok test05_0 (__main__.NcsTestFunctions) NCS Residue Range edit to all chains ... ok test06_0 (__main__.NcsTestFunctions) Manual NCS ghosts generates correct NCS chain ids ... ok test07_0 (__main__.NcsTestFunctions) NCS maps overwrite existing maps ... ok test01_0 (__main__.UtilTestFunctions) Test key symbols ... ok test02_0 (__main__.UtilTestFunctions) Test running a scheme function ... ok test03_0 (__main__.UtilTestFunctions) Internal/External Molecule Numbers match ... ok test05_0 (__main__.UtilTestFunctions) Import gobject ... ok test_00 (__main__.InternalTestFunctions) Test internal functions ... ok ---------------------------------------------------------------------- Ran 125 tests in 276.260s OK Unitest skip does not exist! The following tests were skipped and marked as passed: Libcif horne Make a glycosidic linkage Pyrogen Runs OK? pyrogen dictionary does not make double-quoted atom names INFO:: Command: (close-molecule 0) INFO:: Command: (close-molecule 1) INFO:: Command: (close-molecule 2) INFO:: Command: (close-molecule 3) INFO:: Command: (close-molecule 4) INFO:: Command: (close-molecule 5) INFO:: Command: (close-molecule 6) INFO:: Command: (close-molecule 7) INFO:: Command: (close-molecule 8) INFO:: Command: (close-molecule 9) INFO:: Command: (close-molecule 10) INFO:: Command: (close-molecule 11) INFO:: Command: (close-molecule 13) INFO:: Command: (close-molecule 14) INFO:: Command: (close-molecule 15) INFO:: Command: (close-molecule 16) INFO:: Command: (close-molecule 17) INFO:: Command: (close-molecule 18) INFO:: Command: (close-molecule 21) INFO:: Command: (close-molecule 22) INFO:: Command: (close-molecule 23) INFO:: Command: (close-molecule 24) INFO:: Command: (close-molecule 25) INFO:: Command: (close-molecule 26) INFO:: Command: (close-molecule 27) INFO:: Command: (close-molecule 28) INFO:: Command: (close-molecule 29) INFO:: Command: (close-molecule 30) INFO:: Command: (close-molecule 31) INFO:: Command: (close-molecule 32) INFO:: Command: (close-molecule 33) INFO:: Command: (close-molecule 34) INFO:: Command: (close-molecule 35) INFO:: Command: (close-molecule 36) INFO:: Command: (close-molecule 37) INFO:: Command: (close-molecule 38) INFO:: Command: (close-molecule 39) INFO:: Command: (close-molecule 40) INFO:: Command: (close-molecule 41) INFO:: Command: (close-molecule 44) INFO:: Command: (close-molecule 45) INFO:: Command: (close-molecule 46) INFO:: Command: (close-molecule 47) INFO:: Command: (close-molecule 48) INFO:: Command: (close-molecule 49) INFO:: Command: (close-molecule 50) INFO:: Command: (close-molecule 51) INFO:: Command: (close-molecule 52) INFO:: Command: (close-molecule 53) INFO:: Command: (close-molecule 54) INFO:: Command: (close-molecule 55) INFO:: Command: (close-molecule 56) INFO:: Command: (close-molecule 57) INFO:: Command: (close-molecule 58) INFO:: Command: (close-molecule 59) INFO:: Command: (close-molecule 60) INFO:: Command: (close-molecule 61) INFO:: Command: (close-molecule 62) INFO:: Command: (close-molecule 63) INFO:: Command: (close-molecule 64) INFO:: Command: (close-molecule 65) INFO:: Command: (close-molecule 66) INFO:: Command: (close-molecule 67) INFO:: Command: (close-molecule 68) INFO:: Command: (close-molecule 69) INFO:: Command: (close-molecule 70) INFO:: Command: (close-molecule 71) INFO:: Command: (close-molecule 72) INFO:: Command: (close-molecule 73) INFO:: Command: (close-molecule 74) INFO:: Command: (close-molecule 75) INFO:: Command: (close-molecule 76) INFO:: Command: (close-molecule 77) INFO:: Command: (close-molecule 78) INFO:: Command: (close-molecule 79) INFO:: Command: (close-molecule 80) INFO:: Command: (close-molecule 81) INFO:: Command: (close-molecule 82) INFO:: Command: (close-molecule 83) INFO:: Command: (close-molecule 84) INFO:: Command: (close-molecule 85) INFO:: Command: (close-molecule 86) INFO:: Command: (close-molecule 87) INFO:: Command: (close-molecule 88) INFO:: Command: (close-molecule 89) INFO:: Command: (close-molecule 90) INFO:: Command: (close-molecule 91) INFO:: Command: (close-molecule 92) INFO:: Command: (close-molecule 93) INFO:: Command: (close-molecule 94) INFO:: Command: (close-molecule 97) INFO:: Command: (close-molecule 98) INFO:: Command: (close-molecule 99) INFO:: Command: (close-molecule 101) INFO:: Command: (close-molecule 102) INFO:: Command: (close-molecule 103) INFO:: Command: (close-molecule 104) INFO:: Command: (close-molecule 105) INFO:: Command: (close-molecule 106) INFO:: Command: (close-molecule 107) INFO:: Command: (close-molecule 108) INFO:: Command: (close-molecule 109) INFO:: Command: (close-molecule 110) INFO:: Command: (close-molecule 111) INFO:: Command: (close-molecule 112) INFO:: Command: (close-molecule 113) INFO:: Command: (close-molecule 114) INFO:: Command: (close-molecule 115) INFO:: Command: (close-molecule 116) INFO:: Command: (close-molecule 117) INFO:: Command: (close-molecule 118) INFO:: Command: (close-molecule 119) INFO:: Command: (close-molecule 120) INFO:: Command: (close-molecule 121) INFO:: Command: (close-molecule 122) INFO:: Command: (close-molecule 123) INFO:: Command: (close-molecule 124) INFO:: Command: (close-molecule 125) INFO:: Command: (close-molecule 126) INFO:: Command: (close-molecule 127) INFO:: Command: (close-molecule 128) INFO:: Command: (close-molecule 129) INFO:: Command: (close-molecule 130) INFO:: Command: (close-molecule 131) INFO:: Command: (close-molecule 132) INFO:: Command: (close-molecule 133) INFO:: Command: (close-molecule 134) INFO:: Command: (close-molecule 135) INFO:: Command: (close-molecule 136) INFO:: Command: (close-molecule 137) INFO:: Command: (close-molecule 138) INFO:: Command: (close-molecule 139) INFO:: Command: (close-molecule 140) INFO:: Command: (close-molecule 141) INFO:: Command: (close-molecule 142) INFO:: Command: (close-molecule 144) INFO:: Command: (close-molecule 146) INFO:: Command: (close-molecule 147) INFO:: Command: (close-molecule 148) INFO:: Command: (close-molecule 149) INFO:: Command: (close-molecule 150) INFO:: Command: (close-molecule 152) INFO:: Command: (close-molecule 153) INFO:: Command: (close-molecule 154) INFO:: Command: (close-molecule 155) INFO:: Command: (close-molecule 156) INFO:: Command: (close-molecule 157) INFO:: Command: (close-molecule 158) INFO:: Command: (close-molecule 159) INFO:: Command: (close-molecule 160) INFO:: Command: (close-molecule 161) gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable gc: collectable FINALLY collect some GARBAGE BL INFO:: no of collected carbage items 6 BL DEBUG:: list of garbage items: (, , ) Detailed information for functions: BL INFO:: garbage item and location: BL INFO:: garbage item and location: INFO:: Command: (use-graphics-interface-state) INFO:: Command: (stereo-mode-state) INFO:: Command: (stereo-mode-state) INFO:: Command: (save-state) Good morning Paul Emsley PI Garib Murshudov added 28092012. Welcome to Coot 0.8.9-pre. ObjectCache: Leaked 0003 refs to ObjectCache: Leaked 0003 refs to test_coot_python: coot test passed