testing with greg testing with greg currently we are here: /home/emsley/autobuild/building/pc_2015-09-05__T03_40_09/test-tar/coot-Linux-x86_64-rhel-6-gtk2-python Sat Sep 5 04:47:52 BST 2015 WARNING:: ccp4 setup file setup-ccp4 does not exist. /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/ There are 142 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/AR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HOH.cif INFO:: Reading coordinate file: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Importing python module coot using command from coot import * INFO:: coot.py imported Running python script /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Loading: redefine_functions.py Loading: coot_utils.py Loading: filter.py Loading: coot_lsq.py Loading: shelx.py Loading: get_ebi.py INFO:: Creating directory coot-download Loading: local_code.py Loading: hello.py Good Morning None, Welcome to Coot. 0.8.3-pre (set-display-intro-string "Good Morning None, Welcome to Coot. 0.8.3-pre") Loading: mutate.py Loading: refmac.py Loading: libcheck.py Loading: gap.py Loading: fitting.py Loading: raster3d.py Loading: povray.py Loading: remote_control.py Loading: generic_objects.py Loading: ncs.py Loading: parse_pisa_xml.py Loading: cns2coot.py Loading: clear_backup.py Loading: tips.py Loading: prodrg_import.py Loading: dictionary_generators.py Loading: jligand.py Loading: americanisms.py Loading: group_settings.py Loading: brute_lsqman.py INFO:: loading preferences file /home/emsley/.coot-preferences/chain-colour-mode.py Running python script /home/emsley/.coot-preferences/chain-colour-mode.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/scheme (set-display-intro-string "Good morning Paul. Welcome to Coot") (set-display-lists-for-maps 0) INFO:: loading preferences file /home/emsley/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 0) (unset-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 13.00) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 0) (set-idle-function-rotate-angle 1.00) INFO:: loading preferences file /home/emsley/.coot-preferences/enhanced-ligand.scm INFO:: loading preferences file /home/emsley/.coot-preferences/extra-keys.scm INFO:: loading preferences file /home/emsley/.coot-preferences/key-bindings.scm INFO:: loading preferences file /home/emsley/.coot-preferences/mogul-interface.scm INFO:: loading preferences file /home/emsley/.coot-preferences/morph-residues-gui.scm INFO:: loading preferences file /home/emsley/.coot-preferences/raster3d.scm INFO:: loading preferences file /home/emsley/.coot-preferences/test-fit-step.scm INFO:: loading preferences file /home/emsley/.coot-preferences/use-pyrogen.scm (filter-fileselection-filenames-state) (get-active-map-drag-flag) Loading ~/.coot...done. INFO:: There are 1 command line scripts to run command-line-greg.scm INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary Molecule number -5 is not a valid model molecule INFO:: Reading coordinate file: /home/emsley/data/greg-data/2WF6.cif mmCIF file /home/emsley/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 1 read successfully DEBUG:: there were 3 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "ALF" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ALF.cif INFO:: using standard CCP4 Refmac dictionary to search for "MG" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MG.cif INFO:: using standard CCP4 Refmac dictionary to search for "BG6" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/b/BG6.cif in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Reading coordinate file: /home/emsley/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/emsley/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 2 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Creating directory coot-backup INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Sat_Sep__5_04:47:55_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Sat_Sep__5_04:47:55_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Sat_Sep__5_04:47:55_2015_modification_2.pdb.gz WARNING:: Error reading bogus.map Read map bogus.map failed WARNING:: Can't find file bogus.mtz INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.033 seconds to read MTZ file INFO:: 0.036 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.054 seconds for contour map INFO:: 0.166 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/emsley/data/greg-data/broken.mtz INFO:: not an mtz file: /home/emsley/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.025 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.22866e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.051 seconds for contour map INFO:: 0.12 seconds in total INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 96, 128, 132) INFO:: 0.022 seconds to read MTZ file INFO:: 0.019 seconds to initialize map INFO:: 0.03 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.83254e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.77531 Map minimum: ..... -1.05473 INFO:: 0.01 seconds for contour map INFO:: 0.091 seconds in total INFO:: map file type was determined to be CCP4 type attempting to read CCP4 map: test-3hfl.map closing CCP4 map: test-3hfl.map Map statistics: mean: 1.83254e-11 st.d: 0.260405 Map statistics: min: -1.05473, max: 1.77531 -1.01936 1 -0.948606 16 -0.877855 66 -0.807104 242 -0.736353 732 -0.665602 1945 -0.594851 4226 -0.5241 8607 -0.453349 15185 -0.382598 23838 -0.311847 34975 -0.241096 51260 -0.170345 75439 -0.0995937 108220 -0.0288427 131057 0.0419084 120860 0.112659 80202 0.18341 42617 0.254161 23468 0.324912 17082 0.395663 14264 0.466414 12492 0.537165 10884 0.607916 9094 0.678667 7521 0.749418 5689 0.820169 4124 0.89092 2846 0.961672 1799 1.03242 1021 1.10317 604 1.17392 269 1.24468 145 1.31543 98 1.38618 59 1.45693 26 1.52768 17 1.59843 8 1.66918 7 1.73993 3 1.81068 0 INFO:: n grid points: 811008 INFO:: mean before filtering: 1.83254e-11 INFO:: variance before filtering: 0.0678109 INFO:: filter by ignoring 596 of 811008 counts ( = 0.07349%) with values around -0.007759 from bin 3699 of 10000 Map mean: ........ 5.494e-06 Map rmsd: ........ 0.2604 Map maximum: ..... 1.775 Map minimum: ..... -1.055 WARNING:: Error reading . . is a directory. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 7 read successfully DEBUG:: there were 0 types with no dictionary /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. ERROR 42 READ: Duplicate sequence number and insertion code. LINE #868 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /home/emsley/autobuild/Linux-pc-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb INFO:: 8375 fragments found in total of which 0 were 5 peptides target fragment start res: 10 had 29 db fragment hits, ilength=6 target fragment start res: 13 had 1772 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 16 merge fragments 10 to 20 with 2 fit sets to merge The merging is complete mainchain_fragment from 10 to 20 done mainchain_fragment successfully set cell and symmetry Symmetry available for this molecule INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 9 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 41 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 0 ALA N :: xyz = ( 49.42, 12.37, 4.385) A 0 ALA C :: xyz = ( 50.92, 13, 2.535) A 0 ALA CA :: xyz = ( 50.36, 13.37, 3.907) A 0 ALA O :: xyz = ( 52.12, 13.03, 2.265) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:47:57_2015_modification_0.pdb.gz Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:47:57_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 11 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276 Symmetry available for this molecule Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:47:58_2015_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:47:58_2015_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:47:58_2015_modification_2.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/rotamer-test-fragment.pdb PDB file /home/emsley/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 14 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] INFO:: Reading coordinate file: /home/emsley/data/greg-data/res098.pdb PDB file /home/emsley/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 15 read successfully DEBUG:: there were 0 types with no dictionary created 6 bond restraints created 6 angle restraints created 0 plane restraints created 1 chiral vol restraints created 13 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 9 non-bonded restraints initial distortion_score: 36.32 Initial RMS Z values bonds: 0.4049 angles: 0.4529 torsions: N/A planes: 2.851 non-bonded: 0 chiral vol: 0.1627 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 198) at 10.68 Final Estimated RMS Z Scores: bonds: 0.08647 angles: 0.7939 torsions: N/A planes: 0.8033 non-bonded: 0 chiral vol: 0.6906 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.699 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_res098.pdb_Sat_Sep__5_04:47:59_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 16 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.026 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.037 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.061 seconds for contour map INFO:: 0.134 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:47:59_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:47:59_2015_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 12.05 INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3knw.ent PDB file /home/emsley/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links Symmetry available for this molecule INFO:: NCS chain comparison 185/199 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 18 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "EDO" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/e/EDO.cif INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3knw.ent_Sat_Sep__5_04:47:59_2015_modification_0.pdb.gz load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "redefine-functions.scm" load "json-reader.scm" load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" load "local-code.scm" load "hello.scm" Good morning Paul Emsley. Welcome to Coot 0.8.3-pre. load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "parse-pisa-xml.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "prodrg-import.scm" load "dictionary-generators.scm" load "jligand.scm" load "americanisms.scm" load "group-settings.scm" === greg-tests tests === Loading greg-tests/begin.grg ... =============================================================== ==================== Testing ================================== =============================================================== Loaded greg-tests/begin.grg Running 01-pdb+mtz.scm ... Entered testcase - Post Go To Atom no molecules PASS: Post Go To Atom no molecules Entered testcase - Close bad molecule PASS: Close bad molecule Entered testcase - Read coordinates test PASS: Read coordinates test Entered testcase - New molecule from bogus molecule PASS: New molecule from bogus molecule Entered testcase - Don't crash on empty NCS from mmCIF file closing molecule number 1 PASS: Don't crash on empty NCS from mmCIF file Entered testcase - New molecule from bogus atom selection INFO:: pre-n-molecules 2 post-n-molecules 2 PASS: New molecule from bogus atom selection Entered testcase - ins code change and Goto atom over an ins code break pre and post ins codes: "" "A" pass: ("A" 68 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "A" " CA ") pass: ("A" 68 "" " CA ") pass: ("A" 66 "" " CA ") PASS: ins code change and Goto atom over an ins code break Entered testcase - Read a bogus map PASS: Read a bogus map Entered testcase - Read MTZ test PASS: Read MTZ test Entered testcase - Auto-read bad MTZ test got status: #() got status: #() PASS: Auto-read bad MTZ test Entered testcase - Map Sigma INFO:: map sigmas 0.311500996351242 #f PASS: Map Sigma Entered testcase - Another Level Test PASS: Another Level Test Entered testcase - Sharpen map from map PASS: Sharpen map from map Entered testcase - db-main makes mainchain PASS: db-main makes mainchain Entered testcase - Set Atom Attribute Test PASS: Set Atom Attribute Test Entered testcase - Add Terminal Residue Test PASS: Add Terminal Residue Test Entered testcase - Adding residue by phi psi, no crash PASS: Adding residue by phi psi, no crash Entered testcase - Select by Sphere Sphere mol: there are 4 residues in chain "B" Found 20 sphere atoms PASS: Select by Sphere Entered testcase - Test Views PASS: Test Views Entered testcase - Label Atoms and Delete PASS: Label Atoms and Delete Entered testcase - Rotamer outliers PASS: Rotamer outliers Entered testcase - Alt Conf Occ Sum Reset For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 PASS: Alt Conf Occ Sum Reset Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue PASS: Correct occupancies after auto-fit rotamer on alt-confed residue Entered testcase - Rotamers work on MSE se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746)) se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616)) PASS: Rotamers work on MSEINFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 19 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1py3.ent_Sat_Sep__5_04:48:00_2015_modification_0.pdb.gz INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP INFO:: 25 residues had their atoms swapped INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 20 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.037 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.056 seconds for contour map INFO:: 0.13 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:00_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: Reading coordinate file: /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-pepflip-test.pdb_Sat_Sep__5_04:48:00_2015_modification_0.pdb.gz flipped 65 A INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 23 read successfully DEBUG:: there were 0 types with no dictionary in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x3e44910 omega: 1 12.77 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:48:01_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:48:01_2015_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 flipped 11 A INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:48:01_2015_modification_2.pdb.gz created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 31 non-bonded restraints initial distortion_score: 2094 Initial RMS Z values bonds: 15.47 angles: 7.387 torsions: N/A planes: 6.517 non-bonded: 48.74 chiral vol: 3.045 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 73) at -4806 Final Estimated RMS Z Scores: bonds: 1.964 angles: 1.368 torsions: N/A planes: 3.39 non-bonded: 1.573 chiral vol: 0.2692 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.748 Refinement elapsed time: 0.015 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:48:01_2015_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:48:01_2015_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:48:01_2015_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.732 created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 71 non-bonded restraints initial distortion_score: -5944 Initial RMS Z values bonds: 1.429 angles: 1.602 torsions: N/A planes: 4.652 non-bonded: 1.507 chiral vol: 0.466 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 54) at -6087 Final Estimated RMS Z Scores: bonds: 1.767 angles: 1.208 torsions: N/A planes: 3.562 non-bonded: 0.6824 chiral vol: 0.09798 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.852 Refinement elapsed time: 0.016 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sat_Sep__5_04:48:01_2015_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 24 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.026 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.054 seconds for contour map INFO:: 0.125 seconds in total created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 6 non-bonded restraints initial distortion_score: -2790 Initial RMS Z values bonds: 1.674 angles: 1.07 torsions: N/A planes: 1.965 non-bonded: 9.246 chiral vol: 1.462 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 17) at -2929 Final Estimated RMS Z Scores: bonds: 1.161 angles: 1.407 torsions: N/A planes: 1.813 non-bonded: 3.146 chiral vol: 0.8141 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.325 Refinement elapsed time: 0.008 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:01_2015_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 26 read successfully DEBUG:: there were 0 types with no dictionary here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:48:02_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 parallel plane restraints Flanking residue restraints: 5 bond links 15 angle links 10 plane links 0 parallel plane restraints INFO:: make_restraints(): made 784 non-bonded restraints initial distortion_score: -1.1e+04 Initial RMS Z values bonds: 1.806 angles: 0.8912 torsions: N/A planes: 2.122 non-bonded: 0.0008065 chiral vol: 0.669 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 31) at -1.121e+04 Final Estimated RMS Z Scores: bonds: 1.065 angles: 0.6838 torsions: N/A planes: 1.529 non-bonded: 0.001635 chiral vol: 0.2457 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.039 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:48:02_2015_modification_1.pdb.gz INFO:: replace_coords: 23 atoms updated. created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints created 84 restraints Link restraints: 4 bond links 12 angle links 8 plane links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 1031 non-bonded restraints initial distortion_score: -1.277e+04 Initial RMS Z values bonds: 0.9807 angles: 1.018 torsions: N/A planes: 9.549 non-bonded: 0.4795 chiral vol: 10.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 26) at -1.617e+04 Final Estimated RMS Z Scores: bonds: 1.67 angles: 1.907 torsions: N/A planes: 1.965 non-bonded: 0.008137 chiral vol: 1.875 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.57 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sat_Sep__5_04:48:02_2015_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 27 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.026 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.064 seconds for contour map INFO:: 0.135 seconds in total created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -8699 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 9) at -1.178e+04 Final Estimated RMS Z Scores: bonds: 1.75 angles: 2.112 torsions: N/A planes: 2.166 non-bonded: 0.02675 chiral vol: 2.055 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.105 Refinement elapsed time: 0.081 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -462.7 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 14) at -2710 Final Estimated RMS Z Scores: bonds: 0.5433 angles: 1.692 torsions: N/A planes: 1.444 non-bonded: 0.01106 chiral vol: 1.261 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.298 Refinement elapsed time: 0.192 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 456.9 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 16) at -1724 Final Estimated RMS Z Scores: bonds: 0.4133 angles: 1.643 torsions: N/A planes: 1.222 non-bonded: 0.007647 chiral vol: 1.261 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.851 Refinement elapsed time: 0.553 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 848.7 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 70) at -1304 Final Estimated RMS Z Scores: bonds: 0.3686 angles: 1.62 torsions: N/A planes: 1.111 non-bonded: 0.006338 chiral vol: 1.255 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.342 Refinement elapsed time: 0.49 INFO:: Reading coordinate file: /home/emsley/data/greg-data/alt-conf-waters.pdb PDB file /home/emsley/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 29 read successfully DEBUG:: there were 0 types with no dictionary masking....masking done INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-waters.pdb_Sat_Sep__5_04:48:05_2015_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Reading coordinate file: /home/emsley/data/greg-data/backrub-fragment.pdb PDB file /home/emsley/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 30 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Sat_Sep__5_04:48:05_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Sat_Sep__5_04:48:05_2015_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/coords-B3A.pdb PDB file /home/emsley/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 32 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "B3A" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/b/B3A.cif created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 2.951 Initial RMS Z values bonds: 0.6619 angles: 0.3737 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.25 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 28) at 4.058e-05 Final Estimated RMS Z Scores: bonds: 0.0005327 angles: 0.002779 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0007482 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 10.29 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Sat_Sep__5_04:48:05_2015_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/lib-B3A.cif not found. init_refmac_mon_lib /home/emsley/data/greg-data/lib-B3A.cif had no bond restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 4.058e-05 Initial RMS Z values bonds: 0.0005327 angles: 0.002779 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0007482 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at 3.068e-05 Final Estimated RMS Z Scores: bonds: 0.0003435 angles: 0.00244 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0005781 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 10.38 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Sat_Sep__5_04:48:05_2015_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. There are 3 data in /home/emsley/data/greg-data/lib-both.cif Welcome to Coot created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 3.019 Initial RMS Z values bonds: 0.6708 angles: 0.3755 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.2535 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 30) at 3.942e-06 Final Estimated RMS Z Scores: bonds: 0.0005906 angles: 0.0006086 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0005886 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 10.46 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Sat_Sep__5_04:48:05_2015_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.027 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.036 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.051 seconds for contour map INFO:: 0.123 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-TER-OXT.pdb PDB file /home/emsley/data/greg-data/test-TER-OXT.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 34 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_test-TER-OXT.pdb_Sat_Sep__5_04:48:06_2015_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.13,-9.09,14.92) B-factor: 45 WARNING:: This residue already has an OXT - aborting INFO:: Reading coordinate file: /home/emsley/data/greg-data/val.pdb PDB file /home/emsley/data/greg-data/val.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 35 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_home_emsley_data_greg-data_val.pdb_Sat_Sep__5_04:48:06_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/2yie-frag.pdb PDB file /home/emsley/data/greg-data/2yie-frag.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_2yie-frag.pdb_Sat_Sep__5_04:48:07_2015_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04043 rms devi: 0.04717 max devi: 0.08328 min devi: 0.01301 INFO:: Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 37 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NCO" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/n/NCO.cif INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Sat_Sep__5_04:48:07_2015_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04346 rms devi: 0.04779 max devi: 0.07399 min devi: 0.01477 INFO:: Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb PDB file /home/emsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 38 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Sat_Sep__5_04:48:07_2015_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.03945 rms devi: 0.04446 max devi: 0.06949 min devi: 0.01513 INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.028 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.037 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.047 seconds for contour map INFO:: 0.122 seconds in total INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.028 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.045 seconds for contour map INFO:: 0.116 seconds in total INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 41 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.001409 st.d: 0.3056 Map statistics: min: -0.9217, max: 3.052 -0.872 10 -0.7727 72 -0.6733 614 -0.574 3970 -0.4746 16922 -0.3753 47064 -0.276 80116 -0.1766 105930 -0.07731 131011 0.02203 142638 0.1214 80192 0.2207 37039 0.32 20148 0.4194 14894 0.5187 11885 0.618 10488 0.7174 8813 0.8167 7252 0.916 5646 1.015 4143 1.115 2992 1.214 2070 1.313 1406 1.413 857 1.512 523 1.611 288 1.711 155 1.81 64 1.909 36 2.009 17 2.108 8 2.207 2 2.307 5 2.406 4 2.505 2 2.605 1 2.704 1 2.803 1 2.903 0 3.002 1 3.101 0 Entered testcase - Hs are correctly swapped on a TYR results: (#t #t #t #t) PASS: Hs are correctly swapped on a TYR Entered testcase - Splitting residue leaves no atoms with negative occupancy PASS: Splitting residue leaves no atoms with negative occupancy Entered testcase - Pepflip flips the correct alt confed atoms PASS: Pepflip flips the correct alt confed atoms Entered testcase - Correction of CISPEP test CISPEPs: "3" PASS: Correction of CISPEP test Entered testcase - Refine Zone with Alt conf refined moved: d=0.293867365894509 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.29249446115313 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 1.750" 1.75016331672668) ("Angles" "Angles: 2.112" 2.1124963760376) ("Planes" "Planes: 2.166" 2.16571426391602) ("Non-bonded" "Non-bonded: 0.164" 0.163565874099731) ("Chirals" "Chirals: 2.055" 2.05520558357239))) ow factor: 2.02089488506317 INFO:: setting refinement weight to 14.6914208942854 refinement results: ("" 0 (("Bonds" "Bonds: 0.543" 0.543342411518097) ("Angles" "Angles: 1.692" 1.69213783740997) ("Planes" "Planes: 1.444" 1.44369614124298) ("Non-bonded" "Non-bonded: 0.105" 0.105189897119999) ("Chirals" "Chirals: 1.261" 1.26075649261475))) ow factor: 1.23498322069645 INFO:: setting refinement weight to 9.63255898156116 refinement results: ("" 0 (("Bonds" "Bonds: 0.413" 0.413261204957962) ("Angles" "Angles: 1.643" 1.64314484596252) ("Planes" "Planes: 1.222" 1.22240495681763) ("Non-bonded" "Non-bonded: 0.087" 0.0874488800764084) ("Chirals" "Chirals: 1.261" 1.26139426231384))) ow factor: 1.13505131751299 INFO:: setting refinement weight to 7.47671240278146 refinement results: ("" 0 (("Bonds" "Bonds: 0.369" 0.36857745051384) ("Angles" "Angles: 1.620" 1.62017297744751) ("Planes" "Planes: 1.111" 1.11148524284363) ("Non-bonded" "Non-bonded: 0.080" 0.0796118378639221) ("Chirals" "Chirals: 1.255" 1.25538265705109))) ow factor: 1.08890458196402 PASS: Refinement gives useful results Entered testcase - Rigid Body Refine Alt Conf Waters PASS: Rigid Body Refine Alt Conf Waters Entered testcase - Setting multiple atom attributes PASS: Setting multiple atom attributes Entered testcase - Tweak Alt Confs on Active Residue PASS: Tweak Alt Confs on Active Residue Entered testcase - Backrub rotamer PASS: Backrub rotamer Entered testcase - Libcif horne PASS: Libcif horne Entered testcase - Refmac Parameters Storage PASS: Refmac Parameters Storage Entered testcase - OXT is added before TER record - add only one found TER "TER 25 ASP A 14 " PASS: OXT is added before TER record - add only one Entered testcase - The position of the oxygen after a mutation PASS: The position of the oxygen after a mutation Entered testcase - TER is at the end of a nucleotide after mutation PASS: TER is at the end of a nucleotide after mutation Entered testcase - C7 is removed on mutation from a DC PASS: C7 is removed on mutation from a DC Entered testcase - C7 is added on mutation to a DC DEBUG:: atoms is (" P " " OP1" " OP2" " O5'" " C5'" " C4'" " O4'" " C3'" " O3'" " C2'" " C1'" " N1 " " C2 " " N3 " " C4 " " C5 " " C6 " " O2 " " O4 " " C7 ") PASS: C7 is added on mutation to a DC Entered testcase - Mask and difference map high-values: (0.989829301834106 0.952502369880676 1.01570284366608 0.636203646659851 0.687578678131104 0.801753640174866 0.738103628158569 1.06824910640717 1.01713156700134 1.01199650764465 0.822739899158478) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) Map statistics: mean: -0.001409 st.d: 0.0605 Map statistics: min: -2.993, max: 0.7743 -2.946 2 -2.851 2 -2.757 1 -2.663 2 -2.569 3 -2.475 3 -2.381 1 -2.286 4 -2.192 4 -2.098 3 -2.004 4 -1.91 4 -1.816 6 -1.721 12 -1.627 20 -1.533 21 -1.439 29 -1.345 47 -1.25 87 -1.156 85 -1.062 153 -0.968 182 -0.8738 266 -0.7796 331 -0.6854 378 -0.5912 415 -0.4971 517 -0.4029 588 -0.3087 704 -0.2145 858 -0.1204 1154 -0.02619 723063 0.06799 2120 0.1622 2190 0.2563 1772 0.3505 1353 0.4447 623 0.5389 215 0.6331 49 0.7272 9 0.8214 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: (-0.893179178237915 -0.947303891181946 -1.18386626243591 -1.29074656963348 -1.08600687980652 -0.827113330364227 -0.848896384239197 -0.693203151226044 -0.970726788043976 -0.553648889064789) INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.026 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.036 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.049 seconds for contour map INFO:: 0.12 seconds in total INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.027 seconds to read MTZ file INFO:: 0.051 seconds to initialize map INFO:: 0.051 seconds for FFT INFO:: 0.012 seconds for statistics Map mean: ........ 1.161e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.071 Map minimum: ..... -0.8775 INFO:: 0.064 seconds for contour map INFO:: 0.205 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 160, 192, 96) by 1 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1 Map statistics: mean: -3.347e-06 st.d: 0.311 Map statistics: min: -0.9165, max: 3.052 -0.8669 10 -0.7677 76 -0.6685 693 -0.5693 4378 -0.4701 18338 -0.3709 49769 -0.2717 82935 -0.1725 109167 -0.07332 133898 0.02588 127242 0.1251 79379 0.2243 36898 0.3235 20503 0.4227 15332 0.5219 12363 0.6211 10886 0.7203 9118 0.8195 7521 0.9187 5833 1.018 4256 1.117 3092 1.216 2109 1.315 1444 1.415 867 1.514 533 1.613 302 1.712 160 1.811 68 1.911 40 2.01 20 2.109 11 2.208 7 2.308 9 2.407 5 2.506 5 2.605 4 2.704 2 2.804 4 2.903 1 3.002 2 3.101 0 Map statistics: mean: 3.348e-06 st.d: 0.001086 Map statistics: min: -0.01092, max: 0.009508 -0.01066 1 -0.01015 4 -0.009643 5 -0.009133 7 -0.008622 8 -0.008111 17 -0.007601 17 -0.00709 20 -0.006579 18 -0.006069 43 -0.005558 95 -0.005047 231 -0.004536 544 -0.004026 1166 -0.003515 2162 -0.003004 4144 -0.002494 8444 -0.001983 16359 -0.001472 32958 -0.0009615 73386 -0.0004508 158314 5.992e-05 204518 0.0005706 125581 0.001081 51957 0.001592 23884 0.002103 12695 0.002613 7551 0.003124 4844 0.003635 3115 0.004146 1977 0.004656 1264 0.005167 844 0.005678 507 0.006188 274 0.006699 169 0.00721 74 0.00772 47 0.008231 18 0.008742 10 0.009253 8 0.009763 0 INFO:: Reading coordinate file: /home/emsley/data/greg-data/multi-carbo-coot-2.pdb PDB file /home/emsley/data/greg-data/multi-carbo-coot-2.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 48 read successfully DEBUG:: there were 2 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "FUC" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/f/FUC.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/n/NAG.cif created 46 bond restraints created 82 angle restraints created 2 plane restraints created 8 chiral vol restraints created 138 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A INFO:: glycosidic_linkage type :ALPHA1-4: Link restraints: 1 bond links 3 angle links 0 plane links 0 parallel plane restraints INFO:: make_restraints(): made 671 non-bonded restraints initial distortion_score: 7037 Initial RMS Z values bonds: 11.36 angles: 3.259 torsions: N/A planes: 0.08353 non-bonded: 0.09438 chiral vol: 0.9035 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 397) at 0.7474 Final Estimated RMS Z Scores: bonds: 0.02236 angles: 0.09026 torsions: N/A planes: 0.001388 non-bonded: 2.091e-05 chiral vol: 0.04659 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 15.34 debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_emsley_data_greg-data_multi-carbo-coot-2.pdb_Sat_Sep__5_04:48:10_2015_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-VAL.pdb PDB file /home/emsley/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 49 read successfully DEBUG:: there were 0 types with no dictionary created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.997 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.4516 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 80) at 0.2476 Final Estimated RMS Z Scores: bonds: 0.01102 angles: 0.09486 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1448 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 16.04 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:48:11_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 49 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:48:11_2015_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:48:11_2015_modification_0.pdb.gz PDB file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:48:11_2015_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.997 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.4516 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 80) at 0.2476 Final Estimated RMS Z Scores: bonds: 0.01102 angles: 0.09486 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1448 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 16.11 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Sat_Sep__5_04:48:11_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 50 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: 1137 Initial RMS Z values bonds: 5.621 angles: 3.433 torsions: N/A planes: N/A non-bonded: 3.491 chiral vol: 0.7534 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 260) at 0.4735 Final Estimated RMS Z Scores: bonds: 0.009656 angles: 0.1208 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1385 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 17.02 debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_emsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Sat_Sep__5_04:48:12_2015_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. Symmetry available for this molecule created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 28 restraints INFO:: make_restraints(): made 39 non-bonded restraints initial distortion_score: 4023 Initial RMS Z values bonds: 1.152 angles: 0.8476 torsions: N/A planes: 3.056 non-bonded: 116.2 chiral vol: 0.7578 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 76) at -473.8 Final Estimated RMS Z Scores: bonds: 0.439 angles: 0.3707 torsions: N/A planes: 0.3299 non-bonded: 0.02655 chiral vol: 0.1288 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 17.08 Refinement elapsed time: 0.022 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:48:12_2015_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. 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: 3145 Initial RMS Z values bonds: 17.37 angles: 0.3707 torsions: N/A planes: 0.3299 non-bonded: 0 chiral vol: 0.1288 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 23) at -542 Final Estimated RMS Z Scores: bonds: 0.1348 angles: 0.1515 torsions: N/A planes: 0.4239 non-bonded: 0 chiral vol: 0.04565 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 17.11 Refinement elapsed time: 0.017 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:48:12_2015_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. INFO:: wrote mmCIF "coot-test-ala.cif" INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 52 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "ACT" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ACT.cif There are 2 data in /home/emsley/data/greg-data/libcheck_ACT.cif Welcome to Coot WARNING:: bond_restraint_length 4 should be 5 created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 15 restraints INFO:: make_restraints(): made 7 non-bonded restraints initial distortion_score: 5304 Initial RMS Z values bonds: 0.01199 angles: 0.00654 torsions: N/A planes: 0 non-bonded: 755.8 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 16) at -137.7 Final Estimated RMS Z Scores: bonds: 0.03196 angles: 0.1766 torsions: N/A planes: 0.04999 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 17.98 Refinement elapsed time: 0.048 INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-ACT.pdb_Sat_Sep__5_04:48:13_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 53 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_2.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_3.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_4.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_6.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_7.pdb.gz Symmetry available for this molecule Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:14_2015_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 56 read successfully DEBUG:: there were 0 types with no dictionary in new_molecule_by_residue_type_selection Something bad happened - No residues selected in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:15_2015_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 57 read successfully DEBUG:: there were 0 types with no dictionary INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] INFO:: Reading coordinate file: /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 50/87 Molecule 58 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 58 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -0.5 is_nucleic_acid_flag 0 console_output 1 --------------------------------------------------- INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID > target seq: DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 163.5 DEBUG:: s.length() 95 DEBUG:: nSelResidues 87 INFO:: backup file coot-backup/_home_emsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Sat_Sep__5_04:48:17_2015_modification_0.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 The alignment resulted in the following Insertions (coalesced): from 1 to 4 ASP VAL SER from 11 to 14 LEU PRO PRO from 62 to 64 PRO GLY Insertions (singles): [spec: 4 "A" 1 ""] -> ASP [spec: 4 "A" 2 ""] -> VAL [spec: 4 "A" 3 ""] -> SER [spec: 4 "A" 11 ""] -> LEU [spec: 4 "A" 12 ""] -> PRO [spec: 4 "A" 13 ""] -> PRO [spec: 4 "A" 62 ""] -> PRO [spec: 4 "A" 63 ""] -> GLY Deletions: [spec: 4 "A" 24 ""] [spec: 4 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 59 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:17_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 60 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:18_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3hfl.ent PDB file /home/emsley/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 61 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "PCA" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PCA.cif INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.019 seconds to read MTZ file INFO:: 0.008 seconds to initialize map INFO:: 0.012 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 2.004e-11 Map sigma: ....... 0.2604 Map maximum: ..... 1.718 Map minimum: ..... -1.034 INFO:: 0.01 seconds for contour map INFO:: 0.052 seconds in total INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Sat_Sep__5_04:48:19_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.834 INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Sat_Sep__5_04:48:19_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.01207 rms devi: 0.01345 max devi: 0.02142 min devi: 0.003856 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1123 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.0847 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.01198 rms devi: 0.01335 max devi: 0.02126 min devi: 0.003873 INFO:: 5 matched atoms had: mean devi: 0.0002426 rms devi: 0.0002428 max devi: 0.0002567 min devi: 0.0002313 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08456 INFO:: 5 matched atoms had: mean devi: 0.2673 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1124 INFO:: 5 matched atoms had: mean devi: 6.931e-05 rms devi: 6.936e-05 max devi: 7.334e-05 min devi: 6.608e-05 INFO:: 5 matched atoms had: mean devi: 0.01203 rms devi: 0.01341 max devi: 0.02135 min devi: 0.003862 INFO:: 5 matched atoms had: mean devi: 0.0001386 rms devi: 0.0001387 max devi: 0.0001467 min devi: 0.0001322 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.01337 max devi: 0.02129 min devi: 0.003869 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.2703 rms devi: 0.3351 max devi: 0.5361 min devi: 0.08481 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Sat_Sep__5_04:48:19_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Sat_Sep__5_04:48:19_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.3372 max devi: 0.5475 min devi: 0.08176 INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.01207 rms devi: 0.01345 max devi: 0.02142 min devi: 0.003856 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1123 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.0847 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.01198 rms devi: 0.01335 max devi: 0.02126 min devi: 0.003873 INFO:: 5 matched atoms had: mean devi: 0.0002426 rms devi: 0.0002428 max devi: 0.0002567 min devi: 0.0002313 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08456 INFO:: 5 matched atoms had: mean devi: 0.2673 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1124 INFO:: 5 matched atoms had: mean devi: 6.931e-05 rms devi: 6.936e-05 max devi: 7.334e-05 min devi: 6.608e-05 INFO:: 5 matched atoms had: mean devi: 0.01203 rms devi: 0.01341 max devi: 0.02135 min devi: 0.003862 INFO:: 5 matched atoms had: mean devi: 0.0001386 rms devi: 0.0001387 max devi: 0.0001467 min devi: 0.0001322 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.01337 max devi: 0.02129 min devi: 0.003869 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.2703 rms devi: 0.3351 max devi: 0.5361 min devi: 0.08481 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Sat_Sep__5_04:48:19_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Sat_Sep__5_04:48:19_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.3372 max devi: 0.5475 min devi: 0.08176 INFO:: 5 matched atoms had: mean devi: 0.005899 rms devi: 0.00671 max devi: 0.01013 min devi: 0.002581 INFO:: 5 matched atoms had: mean devi: 0.007256 rms devi: 0.007788 max devi: 0.01256 min devi: 0.00456 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08783 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5339 min devi: 0.0879 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.007179 rms devi: 0.0077 max devi: 0.01241 min devi: 0.004575 INFO:: 5 matched atoms had: mean devi: 0.005744 rms devi: 0.006571 max devi: 0.009959 min devi: 0.002425 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08776 INFO:: 5 matched atoms had: mean devi: 0.2677 rms devi: 0.3265 max devi: 0.5055 min devi: 0.1047 INFO:: 5 matched atoms had: mean devi: 0.005854 rms devi: 0.006669 max devi: 0.01008 min devi: 0.002535 INFO:: 5 matched atoms had: mean devi: 0.007225 rms devi: 0.007753 max devi: 0.0125 min devi: 0.004565 INFO:: 5 matched atoms had: mean devi: 0.00581 rms devi: 0.006629 max devi: 0.01003 min devi: 0.00249 INFO:: 5 matched atoms had: mean devi: 0.007194 rms devi: 0.007718 max devi: 0.01244 min devi: 0.004572 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3266 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3365 max devi: 0.5339 min devi: 0.08801 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.09235 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004329 rms devi: 0.004818 max devi: 0.007383 min devi: 0.001862 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.326 max devi: 0.5019 min devi: 0.09266 INFO:: 5 matched atoms had: mean devi: 0.005899 rms devi: 0.00671 max devi: 0.01013 min devi: 0.002581 INFO:: 5 matched atoms had: mean devi: 0.007256 rms devi: 0.007788 max devi: 0.01256 min devi: 0.00456 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08783 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5339 min devi: 0.0879 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.007179 rms devi: 0.0077 max devi: 0.01241 min devi: 0.004575 INFO:: 5 matched atoms had: mean devi: 0.005744 rms devi: 0.006571 max devi: 0.009959 min devi: 0.002425 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08776 INFO:: 5 matched atoms had: mean devi: 0.2677 rms devi: 0.3265 max devi: 0.5055 min devi: 0.1047 INFO:: 5 matched atoms had: mean devi: 0.005854 rms devi: 0.006669 max devi: 0.01008 min devi: 0.002535 INFO:: 5 matched atoms had: mean devi: 0.007225 rms devi: 0.007753 max devi: 0.0125 min devi: 0.004565 INFO:: 5 matched atoms had: mean devi: 0.00581 rms devi: 0.006629 max devi: 0.01003 min devi: 0.00249 INFO:: 5 matched atoms had: mean devi: 0.007194 rms devi: 0.007718 max devi: 0.01244 min devi: 0.004572 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3266 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3365 max devi: 0.5339 min devi: 0.08801 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.09235 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004329 rms devi: 0.004818 max devi: 0.007383 min devi: 0.001862 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sat_Sep__5_04:48:19_2015_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.326 max devi: 0.5019 min devi: 0.09266 Symmetry available for this molecule INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:19_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/some-waters-with-ter.pdb PDB file /home/emsley/data/greg-data/some-waters-with-ter.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 68 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_some-waters-with-ter.pdb_Sat_Sep__5_04:48:20_2015_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule INFO:: Reading coordinate file: /home/emsley/data/greg-data/tm+some-waters.pdb PDB file /home/emsley/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 69 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3115 INFO:: Using density cut-off: 0.623 (2 sigma) (mean -0.03382 stdev: 0.1462) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 1.5 3.6 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 59.88, 3.015, -4.288) is too big to be water INFO:: cluster at xyz = ( 70.02, 19.08, 18.63) is too big to be water INFO:: cluster at xyz = ( 53, 9.031, 20.13) is too big to be water INFO:: found 62 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_emsley_data_greg-data_tm+some-waters.pdb_Sat_Sep__5_04:48:21_2015_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 70 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:22_2015_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: Reading coordinate file: /home/emsley/data/greg-data/water-test-no-cell.pdb PDB file /home/emsley/data/greg-data/water-test-no-cell.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 71 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_water-test-no-cell.pdb_Sat_Sep__5_04:48:25_2015_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /home/emsley/data/greg-data/pathological-water-test.pdb PDB file /home/emsley/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 72 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_pathological-water-test.pdb_Sat_Sep__5_04:48:26_2015_modification_0.pdb.gz INFO:: moved 181 water molecules Symmetry available for this molecule INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.026 seconds to read MTZ file INFO:: 0.012 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.069e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.022 seconds for contour map INFO:: 0.079 seconds in total INFO:: Masking around 58 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 94 ALA N :: xyz = ( 58.42, 2.762, -2.12) A 94 ALA C :: xyz = ( 60.22, 2.538, -3.781) A 94 ALA CA :: xyz = ( 59.68, 2.109, -2.419) A 94 ALA O :: xyz = ( 61.35, 3.018, -3.893) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:26_2015_modification_0.pdb.gz Symmetry available for this molecule DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 75 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 75 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 min devi: 0.1254 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:26_2015_modification_0.pdb.gz PASS: Mask and difference map Entered testcase - Simple Averaged maps INFO:: map sigmas: normal 0.311048001050949 and diff-map: 0.00108590547461063 PASS: Simple Averaged maps Entered testcase - Make a glycosidic linkage bond-length: 2.97694066606539: bond-length: 1.44034108558188: PASS: Make a glycosidic linkage Entered testcase - Test for flying hydrogens on undo PASS: Test for flying hydrogens on undo Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0 PASS: Test for mangling of hydrogen names from a PDB v 3.0 Entered testcase - correct matching dictionary names from test name PASS: correct matching dictionary names from test name Entered testcase - update monomer restraints Bond-length: 2.83565064413323: pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.5151313625289: PASS: update monomer restraints Entered testcase - Write mmCIF restraints correctly PASS: Write mmCIF restraints correctly Entered testcase - Refinement OK with zero bond esd PASS: Refinement OK with zero bond esd Entered testcase - Change Chain IDs and Chain Sorting PASS: Change Chain IDs and Chain Sorting Entered testcase - Replace Fragment distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) PASS: Replace Fragment Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () PASS: Residues in Region of Residue Entered testcase - Residues in region of a point PASS: Residues in region of a point Entered testcase - Empty molecule on type selection PASS: Empty molecule on type selection Entered testcase - Set Rotamer PASS: Set Rotamer Entered testcase - Rotamer names and scores are correct Rotamer 0 : "m-85" 100.0 Rotamer 1 : "t80" 90.1668395996094 Rotamer 2 : "p90" 50.7077865600586 Rotamer 3 : "m -30 " 21.4231548309326 Rotamer 4 : "m -30 " 21.4231548309326 PASS: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions ::::: (58 "A" 1 "") #f #f ::::: (58 "A" 4 "") #t #t ::::: (58 "A" 59 "") #t #t ::::: (58 "A" 60 "") #f #f ::::: (58 "A" 61 "") #f #f ::::: (58 "A" 92 "") #t #t ::::: (58 "A" 94 "") #f #f PASS: Align and mutate a model with deletions Entered testcase - renumbered residues should be in seqnum order PASS: renumbered residues should be in seqnum order Entered testcase - Autofit Rotamer on Residues with Insertion codes PASS: Autofit Rotamer on Residues with Insertion codes Entered testcase - RNA base has correct residue type after mutation mutated base to type "C" - was "A" mutated base to type "Cr" - was "A" PASS: RNA base has correct residue type after mutation Entered testcase - resname from serial number doesnt crash on silly input PASS: resname from serial number doesnt crash on silly input Entered testcase - DNA bases are the correct residue type after mutation mutated base to type "DC" mutated base to type "DG" mutated base to type "DA" mutated base to type "DT" mutated base to type "Cd" mutated base to type "Gd" mutated base to type "Ad" mutated base to type "Td" PASS: DNA bases are the correct residue type after mutation Entered testcase - SegIDs are correct after mutate PASS: SegIDs are correct after mutate Entered testcase - TER on water chain is removed on adding a water by hand PASS: TER on water chain is removed on adding a water by hand Entered testcase - TER on water chain is removed on adding waters automatically PASS: TER on water chain is removed on adding waters automatically Entered testcase - Adding atoms to Many-Chained Molecule PASS: Adding atoms to Many-Chained Molecule Entered testcase - Arrange waters round protein PASS: Arrange waters round protein Entered testcase - Correct Segid After Add Terminal Residue PASS: Correct Segid After Add Terminal Residue Entered testcase - Correct Segid after NCS residue range copy PASS: Correct Segid after NCS residue range copy Entered testcase - Merge Water INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 76 read successfully DEBUG:: there were 0 types with no dictionary 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.6,8.687,12.91) B-factor: 45 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.6,8.687,12.91) B-factor: 45 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.6,8.687,12.91) B-factor: 45 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.6,8.687,12.91) B-factor: 45 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.6,8.687,12.91) B-factor: 45 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.6,8.687,12.91) B-factor: 45 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.6,8.687,12.91) B-factor: 45 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.6,8.687,12.91) B-factor: 45 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.6,8.687,12.91) B-factor: 45 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.6,8.687,12.91) B-factor: 45 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.6,8.687,12.91) B-factor: 45 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.6,8.687,12.91) B-factor: 45 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.6,8.687,12.91) B-factor: 45 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.6,8.687,12.91) B-factor: 45 added to molecule INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 77 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "TAR" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TAR.cif INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 78 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 79 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NPO" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/n/NPO.cif -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0 0 0.3333 pre-trans: 0 0 0 Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule INFO:: Matching/moving molecule number 82 to 81 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.03532 rms devi: 0.03779 max devi: 0.05453 min devi: 0.01668 INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076) INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:29_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 83 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 84 read successfully DEBUG:: there were 0 types with no dictionary INFO:: spacegroup: P 21 21 21 INFO:: spacegroup: C 1 2 1 INFO:: Matching/moving molecule number 83 to 84 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.5023 rms devi: 0.5938 max devi: 1.679 min devi: 0.04318 INFO:: Axis orientation: ( 0.567, -0.7175, 0.4046) INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019) INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:31_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 85 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:48:32_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 86 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/emsley/data/greg-data/2goz-manip.pdb PDB file /home/emsley/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links Symmetry available for this molecule INFO:: NCS chain comparison 10/85 Molecule 87 read successfully DEBUG:: there were 7 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "GDP" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GDP.cif INFO:: using standard CCP4 Refmac dictionary to search for "Gr" INFO:: using standard CCP4 Refmac dictionary to search for "Ar" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/AR.cif INFO:: using standard CCP4 Refmac dictionary to search for "Ur" INFO:: using standard CCP4 Refmac dictionary to search for "Cr" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CR.cif INFO:: using standard CCP4 Refmac dictionary to search for "OMC" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/o/OMC.cif INFO:: using standard CCP4 Refmac dictionary to search for "5BU" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/5/5BU.cif SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.903 13.7 9.237 90 98.21 90 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 88 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.32 34.32 11.09 90 90 90 READ-INS:: Spacegroup: "I 41 2 2" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 89 read successfully INFO:: spacegroup: I 41 2 2 LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.73 77.73 77.73 90 90 90 READ-INS:: Spacegroup: "I 21 3" INFO:: chain has 121 residues Symmetry available for this molecule Molecule 90 read successfully ll: 24 DEBUG:: space group initialised with symbol "I 21 3" in read_data_sm_cif() cell is Cell (77.726,77.726,77.726, 90, 90, 90) in read_data_sm_cif() spg is I 21 3 in read_data_sm_cif() reso is 0.5889 Map statistics: mean: -5.07e-05 st.d: 0.3052 Map statistics: min: -0.781, max: 6.079 -0.6953 231 -0.5238 4724 -0.3523 24910 -0.1808 55291 -0.00927 95241 0.1622 40930 0.3337 7480 0.5052 3968 0.6767 2790 0.8482 2117 1.02 1738 1.191 1221 1.363 888 1.534 595 1.706 355 1.877 240 2.049 137 2.22 97 2.392 62 2.563 46 2.735 17 2.906 17 3.078 13 3.249 10 3.421 7 3.592 1 3.764 3 3.935 7 4.107 2 4.278 5 4.45 1 4.621 2 4.793 2 4.964 0 5.136 1 5.307 0 5.479 0 5.65 0 5.822 0 5.993 1 6.165 0 Map statistics: mean: -1.005e-05 st.d: 0.04681 Map statistics: min: -0.2115, max: 0.6486 -0.2008 7 -0.1793 48 -0.1578 209 -0.1363 787 -0.1148 2257 -0.09325 5676 -0.07175 12730 -0.05025 24380 -0.02874 38191 -0.007239 46229 0.01427 43880 0.03577 32484 0.05727 19420 0.07878 9718 0.1003 4120 0.1218 1677 0.1433 718 0.1648 329 0.1863 133 0.2078 77 0.2293 29 0.2508 11 0.2723 13 0.2938 8 0.3153 2 0.3368 2 0.3583 2 0.3798 1 0.4013 1 0.4228 2 0.4443 2 0.4658 1 0.4873 1 0.5088 1 0.5304 1 0.5519 1 0.5734 0 0.5949 0 0.6164 0 0.6379 2 0.6594 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 WARNING:: invalid molecule (204050) for write_shelx_ins_file WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. Chains PASS: Merge Water Chains Entered testcase - Consolidated merge -------- starting chain list ----------- DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "") DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K") PASS: Consolidated merge Entered testcase - LSQ by atom PASS: LSQ by atom Entered testcase - LSQing changes the space-group and cell to that of the reference molecule PASS: LSQing changes the space-group and cell to that of the reference molecule Entered testcase - set-residue-name sets the correct residue PASS: set-residue-name sets the correct residue Entered testcase - fit-protein-make-specs makes all specs specs: 189 ((86 "A" 1 "") (86 "A" 2 "") (86 "A" 3 "") (86 "A" 4 "") (86 "A" 5 "") (86 "A" 6 "") (86 "A" 7 "") (86 "A" 8 "") (86 "A" 9 "") (86 "A" 10 "") (86 "A" 11 "") (86 "A" 12 "") (86 "A" 13 "") (86 "A" 14 "") (86 "A" 15 "") (86 "A" 16 "") (86 "A" 17 "") (86 "A" 18 "") (86 "A" 19 "") (86 "A" 20 "") (86 "A" 21 "") (86 "A" 22 "") (86 "A" 23 "") (86 "A" 24 "") (86 "A" 25 "") (86 "A" 26 "") (86 "A" 27 "") (86 "A" 28 "") (86 "A" 29 "") (86 "A" 30 "") (86 "A" 31 "") (86 "A" 32 "") (86 "A" 33 "") (86 "A" 34 "") (86 "A" 35 "") (86 "A" 36 "") (86 "A" 37 "") (86 "A" 38 "") (86 "A" 39 "") (86 "A" 40 "") (86 "A" 41 "") (86 "A" 42 "") (86 "A" 43 "") (86 "A" 44 "") (86 "A" 45 "") (86 "A" 46 "") (86 "A" 47 "") (86 "A" 48 "") (86 "A" 49 "") (86 "A" 50 "") (86 "A" 51 "") (86 "A" 52 "") (86 "A" 53 "") (86 "A" 54 "") (86 "A" 55 "") (86 "A" 56 "") (86 "A" 57 "") (86 "A" 58 "") (86 "A" 59 "") (86 "A" 60 "") (86 "A" 61 "") (86 "A" 62 "") (86 "A" 63 "") (86 "A" 64 "") (86 "A" 65 "") (86 "A" 66 "") (86 "A" 67 "") (86 "A" 68 "") (86 "A" 69 "") (86 "A" 70 "") (86 "A" 71 "") (86 "A" 72 "") (86 "A" 73 "") (86 "A" 74 "") (86 "A" 75 "") (86 "A" 76 "") (86 "A" 77 "") (86 "A" 78 "") (86 "A" 79 "") (86 "A" 80 "") (86 "A" 81 "") (86 "A" 82 "") (86 "A" 83 "") (86 "A" 84 "") (86 "A" 85 "") (86 "A" 86 "") (86 "A" 87 "") (86 "A" 88 "") (86 "A" 89 "") (86 "A" 90 "") (86 "A" 91 "") (86 "A" 92 "") (86 "A" 93 "") (86 "B" 1 "") (86 "B" 2 "") (86 "B" 3 "") (86 "B" 4 "") (86 "B" 5 "") (86 "B" 6 "") (86 "B" 7 "") (86 "B" 8 "") (86 "B" 9 "") (86 "B" 10 "") (86 "B" 11 "") (86 "B" 12 "") (86 "B" 13 "") (86 "B" 14 "") (86 "B" 15 "") (86 "B" 16 "") (86 "B" 17 "") (86 "B" 18 "") (86 "B" 19 "") (86 "B" 20 "") (86 "B" 21 "") (86 "B" 22 "") (86 "B" 23 "") (86 "B" 24 "") (86 "B" 25 "") (86 "B" 26 "") (86 "B" 27 "") (86 "B" 28 "") (86 "B" 29 "") (86 "B" 30 "") (86 "B" 31 "") (86 "B" 32 "") (86 "B" 33 "") (86 "B" 34 "") (86 "B" 35 "") (86 "B" 36 "") (86 "B" 37 "") (86 "B" 38 "") (86 "B" 39 "") (86 "B" 40 "") (86 "B" 41 "") (86 "B" 42 "") (86 "B" 43 "") (86 "B" 44 "") (86 "B" 45 "") (86 "B" 46 "") (86 "B" 47 "") (86 "B" 48 "") (86 "B" 49 "") (86 "B" 50 "") (86 "B" 51 "") (86 "B" 52 "") (86 "B" 53 "") (86 "B" 54 "") (86 "B" 55 "") (86 "B" 56 "") (86 "B" 57 "") (86 "B" 58 "") (86 "B" 59 "") (86 "B" 60 "") (86 "B" 61 "") (86 "B" 62 "") (86 "B" 63 "") (86 "B" 64 "") (86 "B" 65 "") (86 "B" 66 "") (86 "B" 67 "") (86 "B" 68 "") (86 "B" 69 "") (86 "B" 70 "") (86 "B" 71 "") (86 "B" 72 "") (86 "B" 73 "") (86 "B" 74 "") (86 "B" 75 "") (86 "B" 76 "") (86 "B" 77 "") (86 "B" 78 "") (86 "B" 79 "") (86 "B" 80 "") (86 "B" 81 "") (86 "B" 82 "") (86 "B" 83 "") (86 "B" 84 "") (86 "B" 85 "") (86 "B" 86 "") (86 "B" 87 "") (86 "B" 88 "") (86 "B" 89 "") (86 "B" 90 "") (86 "B" 91 "") (86 "B" 92 "") (86 "B" 93 "") (86 "B" 94 "") (86 "B" 95 "") (86 "B" 96 "")) PASS: fit-protein-make-specs makes all specs Entered testcase - Phosphate distance in pucker analysis is sane PASS: Phosphate distance in pucker analysis is sane Ended 01-pdb+mtz.scm Running 02-shelx.scm ... Entered testcase - Read small molecule .res file PASS: Read small molecule .res file Entered testcase - Read hollander small molecule .res file PASS: Read hollander small molecule .res file Entered testcase - read shelx insulin with fcf PASS: read shelx insulin with fcf Entered testcase - Write an INS from PDB test PASS: Write an INS from PDB test Entered testcase - new molecule by atom selection inherits Symmetry available for this molecule Symmetry available for this molecule INFO:: Masking around 32 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. B 2021 ALA N :: xyz = ( -11.33, 19.47, 57.91) B 2021 ALA C :: xyz = ( -12.04, 20.27, 60.12) B 2021 ALA CA :: xyz = ( -11.37, 20.62, 58.8) B 2021 ALA O :: xyz = ( -11.44, 20.43, 61.19) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Sat_Sep__5_04:48:34_2015_modification_0.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CD2" INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Sat_Sep__5_04:48:34_2015_modification_0.res 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3052 INFO:: Using density cut-off: 0.1831 (0.6 sigma) (mean -0.02035 stdev: 0.1119) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 1.5 3.6 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water INFO:: found 126 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Sat_Sep__5_04:48:34_2015_modification_1.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O " INFO:: Adding to solvent chain: D LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.14 83.03 89.79 90 90 90 READ-INS:: Spacegroup: "P 21 21 21" INFO:: chain has 5 residues Symmetry available for this molecule Molecule 95 read successfully LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.7 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 96 read successfully INFO:: SHELXL file new-horma.ins written. LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.7 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 97 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 109 109 107.6 90 90 90 READ-INS:: Spacegroup: "I 4 2 2" INFO:: chain has 4 residues Symmetry available for this molecule Molecule 98 read successfully INFO:: Creating directory coot-ccp4 shelx molecule flag PASS: new molecule by atom selection inherits shelx molecule flag Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy Entered testcase - Add water to SHELX molecule PASS: Add water to SHELX molecule Entered testcase - Find Waters for a SHELXL molecule PASS: Find Waters for a SHELXL molecule Entered testcase - NPD Anisotropic Atom [Mitch Miller] PASS: NPD Anisotropic Atom [Mitch Miller] Entered testcase - close shelx molecules PASS: close shelx molecules Entered testcase - Aniso Bs in P21 b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) PASS: Aniso Bs in P21 Entered testcase - Don't crash on reading a strange HAT file PASS: Don't crash on reading a strange HAT file Ended 02-shelx.scm Running 03-ligand.scm ... Entered testcase - Get monomer test run-command-in-dir dir: "coot-ccp4/" exe: "libcheck" cl-args: () data-lines: ("N" "MON 3GP" "") log-file-name: "coot-libcheck-3GP.log" #t : : --- LIBCHECK --- /Vers 5.2.02 ; 02.12.2014/ : : : Do you want to have FILE-DOCUMENT /libcheck.doc/ ? //Y/A : : N - means without DOC-file : Y - with new contents : A - means to keep old contents and add new information : with DOC-file program creates batch file: libcheck.bat : _DOC: : : # : # Keywords: : # : #FILE_L: < > - additional library, " " means without this file : #MON: < > - give info about this monomer : # if = * , give list all monomers in the library : #FILE_PDB: < > - input PDB_file ," " means without this file : #FILE_SMILE: < > - input SMILE_file ," " means without this fil e : #FILE_SDF: < > - input SDF file, " " means without this file : #FILE_MOL: < > - input MOL (sybil), SDF, ODB (O) files : # use keyword MON as compound_id : #FILE_CIF: < > - input CIFile ," " means without this file : #FILE_CSD: < > - input CSD CIFile," " means without this file : #HFLAG: /A/N - Y - hydrogen atoms where they are : # A - with all hydrogen atoms : # N - without hydrogen atoms : #IND: /Y - Y - create index of mon_lib.cif : # output file: "new_mon_lib_ind.cif" : #FILE_O: - output files /library,coords,ps/, name without : # extention : #FILE_L2: < > - additional library (FILE_L) will be added to this library : # in this case program performs only adding : #ANGLE: <0.0> - rotation angle for picture ( around X ) : #LIST: /S/L - S short output, L - long, M - medium : #REF: /S,N,0 - 0 no refinement of new monomer : # N only crd->ang and ang->crd : # S plus torsion ref, Y plus restr.ref : # : #TEST: <0> - for program testing only : #COOR: /Y - use Vobs from coords instead Videal : #LCOOR: /N - Y use coords from lib description : #NODIST: /Y - Y not read the distributed library : # (only with FILE_L) : #SRCH: /Y/0 - Y - global search, 0 - for MON from PDB_file : # (only with NODIST = N) : : #--- type "keyword parameters" and/or --- : #--- press key "CR" to run program --- : --> --> MON : 3GP : ------------- : ------------- : Keywords: : HFLAG : Y : COOR : N : LCOOR : Y : SRCH : N : REF : Y : NODIST: N : ------------------------------ : --- LIBRARY OF MONOMERS --- : _lib_name mon_lib : _lib_version 5.44 : _lib_update 30/05/14 : ------------------------------ : NUMBER OF MONOMERS IN THE LIBRARY : 11608 : with complete description : 11608 : NUMBER OF MODIFICATIONS : 63 : NUMBER OF LINKS : 73 : I am reading libraries. Please wait. : - energy parameters : - monomer"s description (links & mod ) : I am reading library. Please wait. : - monomer"s description : WARNING: bond C4' - C3' delta (lib-coord) : 0.020 : WARNING: bond C3' - C2' delta (lib-coord) : 0.023 : WARNING: bond N9 - C8 delta (lib-coord) : 0.028 : WARNING: bond N9 - C4 delta (lib-coord) : 0.030 : WARNING: bond C8 - N7 delta (lib-coord) : 0.050 : WARNING: bond C5 - C6 delta (lib-coord) : 0.075 : WARNING: bond C5 - C4 delta (lib-coord) : 0.090 : WARNING: bond C6 - O6 delta (lib-coord) : 0.031 : WARNING: bond C2 - N1 delta (lib-coord) : 0.027 : WARNING: bond N3 - C2 delta (lib-coord) : 0.036 : WARNING: angle O4' - C1' - C2' delta (lib-coord) : 4.463 : WARNING: angle C1' - O4' - C4' delta (lib-coord) : 6.546 : WARNING: angle C1' - C2' - C3' delta (lib-coord) : 7.042 : WARNING: angle C2' - C3' - C4' delta (lib-coord) : 6.948 : WARNING: angle C3' - O3' - P delta (lib-coord) : 13.628 : WARNING: angle O3P - P - O2P delta (lib-coord) : 10.426 : WARNING: angle O3P - P - O1P delta (lib-coord) : 10.379 : WARNING: angle O2P - P - O1P delta (lib-coord) : 10.383 : WARNING: angle C3' - C4' - O4' delta (lib-coord) : 4.651 : WARNING: tors O6 - C6 - N1 - C2 delta (lib-coord) : 0.303 : WARNING: tors C6 - N1 - C2 - N3 delta (lib-coord) : 0.636 : WARNING: tors N1 - C2 - N2 - HN21 delta (lib-coord) : 0.000 : WARNING: tors N1 - C2 - N3 - C4 delta (lib-coord) : 0.332 : WARNING: tors C2 - N3 - C4 - N9 delta (lib-coord) : 0.079 : WARNING: tors N3 - C4 - C5 - N7 delta (lib-coord) : 0.034 : WARNING: tors C4 - C5 - C6 - O6 delta (lib-coord) : 0.034 : WARNING: tors C4 - C5 - N7 - C8 delta (lib-coord) : 0.020 : WARNING: tors N3 - C4 - N9 - C1' delta (lib-coord) : 0.059 : WARNING: tors C4 - N9 - C8 - N7 delta (lib-coord) : 0.034 : * CIFile : libcheck_3GP.cif : * PDBfile : libcheck_3GP.pdb : * Plotfile: libcheck_3GP.ps : Output dictionary : mmcif : libcheck.lib : odb : libcheck.odb INFO:: libcheck status: 0 : : :
: : :
: 
: ###############################################################
: ###############################################################
: ###############################################################
: ### CCP4 6.5.015: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
: ###############################################################
: User: emsley  Run date:  5/ 9/2015 Run time: 04:48:37 
:
:
: Please reference: Collaborative Computational Project, Number 4. 2011.
: "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
: as well as any specific reference in the program write-up.
:
:
: $TEXT:Reference1: $$ Main reference $$ 
:   "REFMAC5 for the refinement of macromolecular crystal structures:"
:   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
:   Acta Crystallogr. D67, 355-367
:
: $$
: $SUMMARY :Reference1:  $$ Refmac: $$
: :TEXT:Reference1: $$
:
: $TEXT:Reference2: $$ Secondary reference $$ 
:   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
:   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
:   Acta Crystallogr. D53, 240-255
:   EU  Validation contract: BIO2CT-92-0524
:
: $$
: $SUMMARY :Reference2:  $$ Refmac: $$
: :TEXT:Reference2: $$
:
: Data line--- MODE NEWENTRY
: Data line--- END
:  Data line--- MODE NEWENTRY
:  Data line--- END
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
:
:    ****                     Input and Default parameters#                      ****
:
:
:Input coordinate file.  Logical name - XYZIN actual file name  - coot-ccp4/libcheck_3GP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name - coot-ccp4/monomer-3GP.pdb
:
:  Refinement type                        : Idealisation
:
:    ****                           Makecif parameters                           ****
:
:Dictionary files for restraints : /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/ener_lib.cif
:User supplied dictionary entries: coot-ccp4/libcheck_3GP.cif
:    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
:    Hydrogens will be restored in their riding positions
:    hydrogens will be written to the output file
:    Links between monomers will be checked. Only those links present in the coordinate file will be used
:    Standard sugar links will be analysed and used
:    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
:    Symmetry related links will be analysed and used
:    Cis peptides will be found and used automatically
:
:
:
:
:Monitoring style is "MEDIUM". Complete information will be printed out in the
:first and last cycle. In all other cycles minimum information will be printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will be printed out
:Distance outliers      10.000
:Angle outliers         10.000
:Torsion outliers       10.000
:Chiral volume outliers 10.000
:Plane outliers         10.000
:Non-bonding outliers   10.000
:---------------------------------------------------------------
:
: Input file :coot-ccp4/libcheck_3GP.pdb
:  ------------------------------
:  ---  LIBRARY OF MONOMERS   ---
: _lib_name         mon_lib
: _lib_version      5.44
: _lib_update       30/05/14
:  ------------------------------
:  NUMBER OF MONOMERS IN THE LIBRARY          : 11608
:                with complete description    : 11608
:  NUMBER OF MODIFICATIONS                    :    63
:  NUMBER OF LINKS                            :    73
:  I am reading libraries. Please wait.
:      - energy parameters
:      - monomer"s description (links & mod )
:
:FORMATTED      OLD     file opened on unit  45
:
:Logical name: ATOMSF, Filename: /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/atomsf.lib
:
:
:  WARNING: "SCALE" card is absent in input PDB file
:  Number of atoms    :      24
:  Number of residues :       1
:  Number of chains   :       1
:  I am reading library. Please wait.
:                mon_lib.cif
:  --------------------------------
:  --- title of input coord file ---
:
:  PDB_code:3GP
:  PDB_name:coords of 3GP from prog: libcheck
:  PDB_date:XX-XXX-XX
:  --------------------------------
:  Number of chains                  :       1
:  Total number of monomers          :       1
:  Number of atoms                   :      36
:  Number of missing atoms           :       0
:  Number of rebuilt atoms           :      12
:  Number of unknown atoms           :       0
:  Number of deleted atoms           :       0
:
:
: loop_
:     _atom_type_symbol
:     _atom_type_scat_Cromer_Mann_a1
:     _atom_type_scat_Cromer_Mann_b1
:     _atom_type_scat_Cromer_Mann_a2
:     _atom_type_scat_Cromer_Mann_b2
:     _atom_type_scat_Cromer_Mann_a3
:     _atom_type_scat_Cromer_Mann_b3
:     _atom_type_scat_Cromer_Mann_a4
:     _atom_type_scat_Cromer_Mann_b4
:     _atom_type_scat_Cromer_Mann_c
:
:
:  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
:  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
:  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
:  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
:  P      6.4345   1.9067   4.1791  27.1570   1.7800   0.5260   1.4908  68.1645   1.1149
:
:
: Number of distances         :           0
: Number of angles            :           0
: Number of torsions          :           0
: Number of planes            :           0
: Number of chirals           :           0
: Number of intervals         :           0
:--------------------------------------------------------------------------------
:--------------------------------------------------------------------------------
:                        Standard  External       All
:                Bonds:        36         0        36
:               Angles:        64         0        64
:              Chirals:         4         0         4
:               Planes:         2         0         2
:             Torsions:        20         0        20
:            Intervals:         0         0         0
:--------------------------------------------------------------------------------
:
:
:  Number of harmonic restraints       =            0
:  Number of atoms in special position =            0
: -----------------------------------------------------
:
: chir max =   0.0000000    
: chir_max =   0.0000000       3.0000000       5.0000000    
:
:
:     CGMAT cycle number =      1
:
: function value    101.82433    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.030     0.020
:Bond distances: others                           10     0.001     0.020
:Bond angles  : refined atoms                     40     4.292     3.000
:Bond angles  : others                            24     1.625     3.000
:Chiral centres: refined atoms                     4     0.186     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.005     0.020
:VDW repulsions.others                            12     0.183     0.200
:VDW; torsion: refined_atoms                      14     0.281     0.200
:VDW; torsion.others                              12     0.178     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.24999984E-02
: Gamma decreased to   4.19999994E-02
:
:
: fvalues    0.0000000       101.82433       36.313282       101.82433    
:
:
:     CGMAT cycle number =      2
:
: function value    36.313282    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.010     0.020
:Bond distances: others                           10     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.19999994E-02
: Gamma decreased to   3.24545428E-02
:
:
: fvalues    0.0000000       36.313282       32.770733       36.313282    
:
:
:     CGMAT cycle number =      3
:
: function value    32.770733    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.24545428E-02
: Gamma decreased to   2.37768572E-02
:
:
: fvalues    0.0000000       32.770733       32.165546       32.770733    
:
:
:     CGMAT cycle number =      4
:
: function value    32.165546    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.37768572E-02
: Gamma decreased to   1.58880539E-02
:
:
: fvalues    0.0000000       32.165546       31.749023       32.165546    
:
:
:     CGMAT cycle number =      5
:
: function value    31.749023    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   1.58880539E-02
: Not converging with gamma equal   1.58880539E-02
: Trying gamma equal   5.35391644E-02
: Gamma decreased to   4.60089408E-02
:
:
: fvalues    0.0000000       31.749023       31.600889       31.749023    
:
:
:     CGMAT cycle number =      6
:
: function value    31.600889    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.60089408E-02
: Not converging with gamma equal   4.60089408E-02
: Trying gamma equal   8.19486380E-02
: Not converging with gamma equal   8.19486380E-02
: Trying gamma equal   0.11968531    
: Gamma decreased to   0.11213798    
:
:
: fvalues    0.0000000       31.600889       31.536364       31.600889    
:
:
:     CGMAT cycle number =      7
:
: function value    31.536364    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11213798    
: Gamma decreased to   0.10527676    
:
:
: fvalues    0.0000000       31.536364       31.471638       31.536364    
:
:
:     CGMAT cycle number =      8
:
: function value    31.471638    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10527676    
: Gamma decreased to   9.90392938E-02
:
:
: fvalues    0.0000000       31.471638       31.406364       31.471638    
:
:
:     CGMAT cycle number =      9
:
: function value    31.406364    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.90392938E-02
: Gamma decreased to   9.33688730E-02
:
:
: fvalues    0.0000000       31.406364       31.340563       31.406364    
:
:
:     CGMAT cycle number =     10
:
: function value    31.340563    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.33688730E-02
: Gamma decreased to   8.82139429E-02
:
:
: fvalues    0.0000000       31.340563       31.274326       31.340563    
:
:
:     CGMAT cycle number =     11
:
: function value    31.274326    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   8.82139429E-02
: Gamma decreased to   8.35276395E-02
:
:
: fvalues    0.0000000       31.274326       31.207850       31.274326    
:
:
:     CGMAT cycle number =     12
:
: function value    31.207850    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   8.35276395E-02
: Gamma decreased to   7.92673677E-02
:
:
: fvalues    0.0000000       31.207850       31.141224       31.207850    
:
:
:     CGMAT cycle number =     13
:
: function value    31.141224    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.92673677E-02
: Gamma decreased to   7.53943920E-02
:
:
: fvalues    0.0000000       31.141224       31.074661       31.141224    
:
:
:     CGMAT cycle number =     14
:
: function value    31.074661    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.53943920E-02
: Gamma decreased to   7.18735084E-02
:
:
: fvalues    0.0000000       31.074661       31.008284       31.074661    
:
:
:     CGMAT cycle number =     15
:
: function value    31.008284    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.18735084E-02
: Gamma decreased to   6.86727017E-02
:
:
: fvalues    0.0000000       31.008284       30.942270       31.008284    
:
:
:     CGMAT cycle number =     16
:
: function value    30.942270    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.86727017E-02
: Gamma decreased to   6.57628775E-02
:
:
: fvalues    0.0000000       30.942270       30.876766       30.942270    
:
:
:     CGMAT cycle number =     17
:
: function value    30.876766    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.57628775E-02
: Not converging with gamma equal   6.57628775E-02
: Trying gamma equal   7.96506703E-02
: Gamma decreased to   7.68731087E-02
:
:
: fvalues    0.0000000       30.876766       30.822355       30.876766    
:
:
:     CGMAT cycle number =     18
:
: function value    30.822355    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.68731087E-02
: Gamma decreased to   7.43480548E-02
:
:
: fvalues    0.0000000       30.822355       30.768475       30.822355    
:
:
:     CGMAT cycle number =     19
:
: function value    30.768475    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.43480548E-02
: Gamma decreased to   7.20525533E-02
:
:
: fvalues    0.0000000       30.768475       30.715254       30.768475    
:
:
:     CGMAT cycle number =     20
:
: function value    30.715254    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.20525533E-02
: Gamma decreased to   6.99657351E-02
:
:
: fvalues    0.0000000       30.715254       30.662777       30.715254    
:
:
:     CGMAT cycle number =     21
:
: function value    30.662777    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.99657351E-02
: Gamma decreased to   6.80686235E-02
:
:
: fvalues    0.0000000       30.662777       30.611145       30.662777    
:
:
:     CGMAT cycle number =     22
:
: function value    30.611145    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.80686235E-02
: Gamma decreased to   6.63439780E-02
:
:
: fvalues    0.0000000       30.611145       30.560417       30.611145    
:
:
:     CGMAT cycle number =     23
:
: function value    30.560417    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.63439780E-02
: Gamma decreased to   6.47761226E-02
:
:
: fvalues    0.0000000       30.560417       30.510704       30.560417    
:
:
:     CGMAT cycle number =     24
:
: function value    30.510704    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.47761226E-02
: Gamma decreased to   6.33507967E-02
:
:
: fvalues    0.0000000       30.510704       30.462093       30.510704    
:
:
:     CGMAT cycle number =     25
:
: function value    30.462093    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.33507967E-02
: Not converging with gamma equal   6.33507967E-02
: Trying gamma equal   7.01534897E-02
: Gamma decreased to   6.87929541E-02
:
:
: fvalues    0.0000000       30.462093       30.418858       30.462093    
:
:
:     CGMAT cycle number =     26
:
: function value    30.418858    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.87929541E-02
: Gamma decreased to   6.75560981E-02
:
:
: fvalues    0.0000000       30.418858       30.376587       30.418858    
:
:
:     CGMAT cycle number =     27
:
: function value    30.376587    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.75560981E-02
: Gamma decreased to   6.64316863E-02
:
:
: fvalues    0.0000000       30.376587       30.335243       30.376587    
:
:
:     CGMAT cycle number =     28
:
: function value    30.335243    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.64316863E-02
: Gamma decreased to   6.54094964E-02
:
:
: fvalues    0.0000000       30.335243       30.294954       30.335243    
:
:
:     CGMAT cycle number =     29
:
: function value    30.294954    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.54094964E-02
: Gamma decreased to   6.44802302E-02
:
:
: fvalues    0.0000000       30.294954       30.255678       30.294954    
:
:
:     CGMAT cycle number =     30
:
: function value    30.255678    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.44802302E-02
: Gamma decreased to   6.36354461E-02
:
:
: fvalues    0.0000000       30.255678       30.217442       30.255678    
:
:
:     CGMAT cycle number =     31
:
: function value    30.217442    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.36354461E-02
: Gamma decreased to   6.28674552E-02
:
:
: fvalues    0.0000000       30.217442       30.180283       30.217442    
:
:
:     CGMAT cycle number =     32
:
: function value    30.180283    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.28674552E-02
: Gamma decreased to   6.21692836E-02
:
:
: fvalues    0.0000000       30.180283       30.144108       30.180283    
:
:
:     CGMAT cycle number =     33
:
: function value    30.144108    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.21692836E-02
: Gamma decreased to   6.15345836E-02
:
:
: fvalues    0.0000000       30.144108       30.109032       30.144108    
:
:
:     CGMAT cycle number =     34
:
: function value    30.109032    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.15345836E-02
: Gamma decreased to   6.09575808E-02
:
:
: fvalues    0.0000000       30.109032       30.074951       30.109032    
:
:
:     CGMAT cycle number =     35
:
: function value    30.074951    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.09575808E-02
: Gamma decreased to   6.04330339E-02
:
:
: fvalues    0.0000000       30.074951       30.041904       30.074951    
:
:
:     CGMAT cycle number =     36
:
: function value    30.041904    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.04330339E-02
: Gamma decreased to   5.99561743E-02
:
:
: fvalues    0.0000000       30.041904       30.009834       30.041904    
:
:
:     CGMAT cycle number =     37
:
: function value    30.009834    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.99561743E-02
: Gamma decreased to   5.95226660E-02
:
:
: fvalues    0.0000000       30.009834       29.978809       30.009834    
:
:
:     CGMAT cycle number =     38
:
: function value    29.978809    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.95226660E-02
: Gamma decreased to   5.91285676E-02
:
:
: fvalues    0.0000000       29.978809       29.948734       29.978809    
:
:
:     CGMAT cycle number =     39
:
: function value    29.948734    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.91285676E-02
: Not converging with gamma equal   5.91285676E-02
: Trying gamma equal   6.10094965E-02
: Gamma decreased to   6.06333092E-02
:
:
: fvalues    0.0000000       29.948734       29.920404       29.948734    
:
:
:     CGMAT cycle number =     40
:
: function value    29.920404    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:Bond angles  : refined atoms                     40     2.846     3.000
:Bond angles  : others                            24     0.650     3.000
:Chiral centres: refined atoms                     4     0.028     0.200
:Planar groups: refined atoms                     14     0.000     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             4     0.056     0.200
:VDW; torsion: refined_atoms                      12     0.243     0.200
:VDW; torsion.others                              12     0.067     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal   6.06333092E-02
: Gamma decreased to   6.02913238E-02
:
:
: fvalues    0.0000000       29.920404       29.892975       29.920404    
:
:
:     CGMAT cycle number =      1
:
: function value    29.892975    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:Bond angles  : refined atoms                     40     2.844     3.000
:Bond angles  : others                            24     0.650     3.000
:Chiral centres: refined atoms                     4     0.028     0.200
:Planar groups: refined atoms                     14     0.000     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             4     0.056     0.200
:VDW; torsion: refined_atoms                      12     0.243     0.200
:VDW; torsion.others                              12     0.067     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.24999984E-02
: Not converging with gamma equal   5.24999984E-02
: Trying gamma equal   0.10762499    
: Gamma decreased to   9.65999961E-02
:
:
: fvalues    0.0000000       29.892975       29.877441       29.892975    
:
:
:     CGMAT cycle number =      2
:
: function value    29.877441    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.65999961E-02
: Gamma decreased to   8.65772665E-02
:
:
: fvalues    0.0000000       29.877441       29.860640       29.877441    
:
:
:     CGMAT cycle number =      3
:
: function value    29.860640    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   8.65772665E-02
: Gamma decreased to   7.74656981E-02
:
:
: fvalues    0.0000000       29.860640       29.842512       29.860640    
:
:
:     CGMAT cycle number =      4
:
: function value    29.842512    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.74656981E-02
: Gamma decreased to   6.91824555E-02
:
:
: fvalues    0.0000000       29.842512       29.822935       29.842512    
:
:
:     CGMAT cycle number =      5
:
: function value    29.822935    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.91824555E-02
: Gamma decreased to   6.16522320E-02
:
:
: fvalues    0.0000000       29.822935       29.801739       29.822935    
:
:
:     CGMAT cycle number =      6
:
: function value    29.801739    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.16522320E-02
: Gamma decreased to   5.48065752E-02
:
:
: fvalues    0.0000000       29.801739       29.778870       29.801739    
:
:
:     CGMAT cycle number =      7
:
: function value    29.778870    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.48065752E-02
: Gamma decreased to   4.85832505E-02
:
:
: fvalues    0.0000000       29.778870       29.754221       29.778870    
:
:
:     CGMAT cycle number =      8
:
: function value    29.754221    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.85832505E-02
: Not converging with gamma equal   4.85832505E-02
: Trying gamma equal   7.82854706E-02
: Gamma decreased to   7.23450258E-02
:
:
: fvalues    0.0000000       29.754221       29.737091       29.754221    
:
:
:     CGMAT cycle number =      9
:
: function value    29.737091    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.23450258E-02
: Gamma decreased to   6.69446215E-02
:
:
: fvalues    0.0000000       29.737091       29.719170       29.737091    
:
:
:     CGMAT cycle number =     10
:
: function value    29.719170    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.69446215E-02
: Gamma decreased to   6.20351620E-02
:
:
: fvalues    0.0000000       29.719170       29.700369       29.719170    
:
:
:     CGMAT cycle number =     11
:
: function value    29.700369    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.20351620E-02
: Gamma decreased to   5.75720184E-02
:
:
: fvalues    0.0000000       29.700369       29.680782       29.700369    
:
:
:     CGMAT cycle number =     12
:
: function value    29.680782    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.75720184E-02
: Gamma decreased to   5.35146147E-02
:
:
: fvalues    0.0000000       29.680782       29.660429       29.680782    
:
:
:     CGMAT cycle number =     13
:
: function value    29.660429    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.35146147E-02
: Gamma decreased to   4.98260669E-02
:
:
: fvalues    0.0000000       29.660429       29.639355       29.660429    
:
:
:     CGMAT cycle number =     14
:
: function value    29.639355    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.98260669E-02
: Not converging with gamma equal   4.98260669E-02
: Trying gamma equal   6.74305037E-02
: Gamma decreased to   6.39096200E-02
:
:
: fvalues    0.0000000       29.639355       29.622938       29.639355    
:
:
:     CGMAT cycle number =     15
:
: function value    29.622938    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.39096200E-02
: Gamma decreased to   6.07088134E-02
:
:
: fvalues    0.0000000       29.622938       29.606110       29.622938    
:
:
:     CGMAT cycle number =     16
:
: function value    29.606110    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.07088134E-02
: Gamma decreased to   5.77989891E-02
:
:
: fvalues    0.0000000       29.606110       29.588955       29.606110    
:
:
:     CGMAT cycle number =     17
:
: function value    29.588955    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.77989891E-02
: Gamma decreased to   5.51536940E-02
:
:
: fvalues    0.0000000       29.588955       29.571524       29.588955    
:
:
:     CGMAT cycle number =     18
:
: function value    29.571524    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.51536940E-02
: Gamma decreased to   5.27488813E-02
:
:
: fvalues    0.0000000       29.571524       29.553860       29.571524    
:
:
:     CGMAT cycle number =     19
:
: function value    29.553860    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.27488813E-02
: Gamma decreased to   5.05626872E-02
:
:
: fvalues    0.0000000       29.553860       29.536018       29.553860    
:
:
:     CGMAT cycle number =     20
:
: function value    29.536018    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.05626872E-02
: Not converging with gamma equal   5.05626872E-02
: Trying gamma equal   6.09967932E-02
: Gamma decreased to   5.89099713E-02
:
:
: fvalues    0.0000000       29.536018       29.520916       29.536018    
:
:
:     CGMAT cycle number =     21
:
: function value    29.520916    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.89099713E-02
: Gamma decreased to   5.70128597E-02
:
:
: fvalues    0.0000000       29.520916       29.505806       29.520916    
:
:
:     CGMAT cycle number =     22
:
: function value    29.505806    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.70128597E-02
: Gamma decreased to   5.52882142E-02
:
:
: fvalues    0.0000000       29.505806       29.490562       29.505806    
:
:
:     CGMAT cycle number =     23
:
: function value    29.490562    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.52882142E-02
: Gamma decreased to   5.37203550E-02
:
:
: fvalues    0.0000000       29.490562       29.475359       29.490562    
:
:
:     CGMAT cycle number =     24
:
: function value    29.475359    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.37203550E-02
: Gamma decreased to   5.22950292E-02
:
:
: fvalues    0.0000000       29.475359       29.460224       29.475359    
:
:
:     CGMAT cycle number =     25
:
: function value    29.460224    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.22950292E-02
: Gamma decreased to   5.09992763E-02
:
:
: fvalues    0.0000000       29.460224       29.445110       29.460224    
:
:
:     CGMAT cycle number =     26
:
: function value    29.445110    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.09992763E-02
: Gamma decreased to   4.98213209E-02
:
:
: fvalues    0.0000000       29.445110       29.430086       29.445110    
:
:
:     CGMAT cycle number =     27
:
: function value    29.430086    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.98213209E-02
: Gamma decreased to   4.87504527E-02
:
:
: fvalues    0.0000000       29.430086       29.415245       29.430086    
:
:
:     CGMAT cycle number =     28
:
: function value    29.415245    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.87504527E-02
: Gamma decreased to   4.77769338E-02
:
:
: fvalues    0.0000000       29.415245       29.400536       29.415245    
:
:
:     CGMAT cycle number =     29
:
: function value    29.400536    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.77769338E-02
: Not converging with gamma equal   4.77769338E-02
: Trying gamma equal   5.24232686E-02
: Gamma decreased to   5.14940023E-02
:
:
: fvalues    0.0000000       29.400536       29.387175       29.400536    
:
:
:     CGMAT cycle number =     30
:
: function value    29.387175    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.14940023E-02
: Gamma decreased to   5.06492145E-02
:
:
: fvalues    0.0000000       29.387175       29.373995       29.387175    
:
:
:     CGMAT cycle number =     31
:
: function value    29.373995    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.06492145E-02
: Gamma decreased to   4.98812273E-02
:
:
: fvalues    0.0000000       29.373995       29.360981       29.373995    
:
:
:     CGMAT cycle number =     32
:
: function value    29.360981    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.98812273E-02
: Gamma decreased to   4.91830558E-02
:
:
: fvalues    0.0000000       29.360981       29.348146       29.360981    
:
:
:     CGMAT cycle number =     33
:
: function value    29.348146    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.91830558E-02
: Gamma decreased to   4.85483557E-02
:
:
: fvalues    0.0000000       29.348146       29.335510       29.348146    
:
:
:     CGMAT cycle number =     34
:
: function value    29.335510    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.85483557E-02
: Gamma decreased to   4.79713529E-02
:
:
: fvalues    0.0000000       29.335510       29.323067       29.335510    
:
:
:     CGMAT cycle number =     35
:
: function value    29.323067    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.79713529E-02
: Gamma decreased to   4.74468060E-02
:
:
: fvalues    0.0000000       29.323067       29.310829       29.323067    
:
:
:     CGMAT cycle number =     36
:
: function value    29.310829    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.74468060E-02
: Gamma decreased to   4.69699465E-02
:
:
: fvalues    0.0000000       29.310829       29.298843       29.310829    
:
:
:     CGMAT cycle number =     37
:
: function value    29.298843    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.69699465E-02
: Gamma decreased to   4.65364382E-02
:
:
: fvalues    0.0000000       29.298843       29.287045       29.298843    
:
:
:     CGMAT cycle number =     38
:
: function value    29.287045    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.65364382E-02
: Gamma decreased to   4.61423397E-02
:
:
: fvalues    0.0000000       29.287045       29.275482       29.287045    
:
:
:     CGMAT cycle number =     39
:
: function value    29.275482    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.61423397E-02
: Gamma decreased to   4.57840674E-02
:
:
: fvalues    0.0000000       29.275482       29.264126       29.275482    
:
:
:     CGMAT cycle number =     40
:
: function value    29.264126    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:Bond angles  : refined atoms                     40     2.783     3.000
:Bond angles  : others                            24     0.651     3.000
:Chiral centres: refined atoms                     4     0.026     0.200
:Planar groups: refined atoms                     14     0.000     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             4     0.057     0.200
:VDW; torsion: refined_atoms                      12     0.243     0.200
:VDW; torsion.others                              12     0.073     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal   4.57840674E-02
: Gamma decreased to   4.54583652E-02
:
:
: fvalues    0.0000000       29.264126       29.253000       29.264126    
:
:
:     CGMAT cycle number =      1
:
: function value    29.253000    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:Bond angles  : refined atoms                     40     2.781     3.000
:Bond angles  : others                            24     0.651     3.000
:Chiral centres: refined atoms                     4     0.026     0.200
:Planar groups: refined atoms                     14     0.000     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             4     0.057     0.200
:VDW; torsion: refined_atoms                      12     0.243     0.200
:VDW; torsion.others                              12     0.073     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.24999984E-02
: Gamma decreased to   4.19999994E-02
:
:
: fvalues    0.0000000       29.253000       29.243635       29.253000    
:
:
:     CGMAT cycle number =      2
:
: function value    29.243635    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.19999994E-02
: Gamma decreased to   3.24545428E-02
:
:
: fvalues    0.0000000       29.243635       29.232248       29.243635    
:
:
:     CGMAT cycle number =      3
:
: function value    29.232248    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.24545428E-02
: Not converging with gamma equal   3.24545428E-02
: Trying gamma equal   7.80123919E-02
: Gamma decreased to   6.89008236E-02
:
:
: fvalues    0.0000000       29.232248       29.226078       29.232248    
:
:
:     CGMAT cycle number =      4
:
: function value    29.226078    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.89008236E-02
: Gamma decreased to   6.06175810E-02
:
:
: fvalues    0.0000000       29.226078       29.219261       29.226078    
:
:
:     CGMAT cycle number =      5
:
: function value    29.219261    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.06175810E-02
: Gamma decreased to   5.30873574E-02
:
:
: fvalues    0.0000000       29.219261       29.211651       29.219261    
:
:
:     CGMAT cycle number =      6
:
: function value    29.211651    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.30873574E-02
: Gamma decreased to   4.62417006E-02
:
:
: fvalues    0.0000000       29.211651       29.203270       29.211651    
:
:
:     CGMAT cycle number =      7
:
: function value    29.203270    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.62417006E-02
: Gamma decreased to   4.00183760E-02
:
:
: fvalues    0.0000000       29.203270       29.193890       29.203270    
:
:
:     CGMAT cycle number =      8
:
: function value    29.193890    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.00183760E-02
: Not converging with gamma equal   4.00183760E-02
: Trying gamma equal   6.97205961E-02
: Gamma decreased to   6.37801513E-02
:
:
: fvalues    0.0000000       29.193890       29.187643       29.193890    
:
:
:     CGMAT cycle number =      9
:
: function value    29.187643    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.37801513E-02
: Gamma decreased to   5.83797470E-02
:
:
: fvalues    0.0000000       29.187643       29.181007       29.187643    
:
:
:     CGMAT cycle number =     10
:
: function value    29.181007    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.83797470E-02
: Gamma decreased to   5.34702875E-02
:
:
: fvalues    0.0000000       29.181007       29.173872       29.181007    
:
:
:     CGMAT cycle number =     11
:
: function value    29.173872    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.34702875E-02
: Gamma decreased to   4.90071438E-02
:
:
: fvalues    0.0000000       29.173872       29.166368       29.173872    
:
:
:     CGMAT cycle number =     12
:
: function value    29.166368    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.90071438E-02
: Gamma decreased to   4.49497402E-02
:
:
: fvalues    0.0000000       29.166368       29.158276       29.166368    
:
:
:     CGMAT cycle number =     13
:
: function value    29.158276    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.49497402E-02
: Gamma decreased to   4.12611924E-02
:
:
: fvalues    0.0000000       29.158276       29.149731       29.158276    
:
:
:     CGMAT cycle number =     14
:
: function value    29.149731    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.12611924E-02
: Not converging with gamma equal   4.12611924E-02
: Trying gamma equal   5.88656291E-02
: Gamma decreased to   5.53447418E-02
:
:
: fvalues    0.0000000       29.149731       29.143272       29.149731    
:
:
:     CGMAT cycle number =     15
:
: function value    29.143272    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.53447418E-02
: Gamma decreased to   5.21439351E-02
:
:
: fvalues    0.0000000       29.143272       29.136520       29.143272    
:
:
:     CGMAT cycle number =     16
:
: function value    29.136520    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.21439351E-02
: Gamma decreased to   4.92341109E-02
:
:
: fvalues    0.0000000       29.136520       29.129520       29.136520    
:
:
:     CGMAT cycle number =     17
:
: function value    29.129520    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.92341109E-02
: Gamma decreased to   4.65888157E-02
:
:
: fvalues    0.0000000       29.129520       29.122269       29.129520    
:
:
:     CGMAT cycle number =     18
:
: function value    29.122269    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.65888157E-02
: Gamma decreased to   4.41840030E-02
:
:
: fvalues    0.0000000       29.122269       29.114811       29.122269    
:
:
:     CGMAT cycle number =     19
:
: function value    29.114811    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.41840030E-02
: Gamma decreased to   4.19978090E-02
:
:
: fvalues    0.0000000       29.114811       29.107105       29.114811    
:
:
:     CGMAT cycle number =     20
:
: function value    29.107105    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.19978090E-02
: Gamma decreased to   4.00103591E-02
:
:
: fvalues    0.0000000       29.107105       29.099218       29.107105    
:
:
:     CGMAT cycle number =     21
:
: function value    29.099218    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.00103591E-02
: Not converging with gamma equal   4.00103591E-02
: Trying gamma equal   4.94959094E-02
: Gamma decreased to   4.75987978E-02
:
:
: fvalues    0.0000000       29.099218       29.092613       29.099218    
:
:
:     CGMAT cycle number =     22
:
: function value    29.092613    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.75987978E-02
: Gamma decreased to   4.58741523E-02
:
:
: fvalues    0.0000000       29.092613       29.085888       29.092613    
:
:
:     CGMAT cycle number =     23
:
: function value    29.085888    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.58741523E-02
: Gamma decreased to   4.43062931E-02
:
:
: fvalues    0.0000000       29.085888       29.079048       29.085888    
:
:
:     CGMAT cycle number =     24
:
: function value    29.079048    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.43062931E-02
: Gamma decreased to   4.28809673E-02
:
:
: fvalues    0.0000000       29.079048       29.072138       29.079048    
:
:
:     CGMAT cycle number =     25
:
: function value    29.072138    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.28809673E-02
: Gamma decreased to   4.15852144E-02
:
:
: fvalues    0.0000000       29.072138       29.065147       29.072138    
:
:
:     CGMAT cycle number =     26
:
: function value    29.065147    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.15852144E-02
: Not converging with gamma equal   4.15852144E-02
: Trying gamma equal   4.77694832E-02
: Gamma decreased to   4.65326309E-02
:
:
: fvalues    0.0000000       29.065147       29.058941       29.065147    
:
:
:     CGMAT cycle number =     27
:
: function value    29.058941    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.65326309E-02
: Gamma decreased to   4.54082191E-02
:
:
: fvalues    0.0000000       29.058941       29.052719       29.058941    
:
:
:     CGMAT cycle number =     28
:
: function value    29.052719    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.54082191E-02
: Gamma decreased to   4.43860255E-02
:
:
: fvalues    0.0000000       29.052719       29.046501       29.052719    
:
:
:     CGMAT cycle number =     29
:
: function value    29.046501    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.43860255E-02
: Gamma decreased to   4.34567593E-02
:
:
: fvalues    0.0000000       29.046501       29.040226       29.046501    
:
:
:     CGMAT cycle number =     30
:
: function value    29.040226    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.34567593E-02
: Gamma decreased to   4.26119715E-02
:
:
: fvalues    0.0000000       29.040226       29.033924       29.040226    
:
:
:     CGMAT cycle number =     31
:
: function value    29.033924    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.26119715E-02
: Not converging with gamma equal   4.26119715E-02
: Trying gamma equal   4.66439128E-02
: Gamma decreased to   4.58375253E-02
:
:
: fvalues    0.0000000       29.033924       29.028139       29.033924    
:
:
:     CGMAT cycle number =     32
:
: function value    29.028139    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.58375253E-02
: Gamma decreased to   4.51044440E-02
:
:
: fvalues    0.0000000       29.028139       29.022421       29.028139    
:
:
:     CGMAT cycle number =     33
:
: function value    29.022421    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.51044440E-02
: Gamma decreased to   4.44380082E-02
:
:
: fvalues    0.0000000       29.022421       29.016649       29.022421    
:
:
:     CGMAT cycle number =     34
:
: function value    29.016649    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.44380082E-02
: Gamma decreased to   4.38321568E-02
:
:
: fvalues    0.0000000       29.016649       29.010910       29.016649    
:
:
:     CGMAT cycle number =     35
:
: function value    29.010910    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.38321568E-02
: Gamma decreased to   4.32813838E-02
:
:
: fvalues    0.0000000       29.010910       29.005224       29.010910    
:
:
:     CGMAT cycle number =     36
:
: function value    29.005224    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.32813838E-02
: Gamma decreased to   4.27806787E-02
:
:
: fvalues    0.0000000       29.005224       28.999550       29.005224    
:
:
:     CGMAT cycle number =     37
:
: function value    28.999550    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.27806787E-02
: Gamma decreased to   4.23254929E-02
:
:
: fvalues    0.0000000       28.999550       28.993898       28.999550    
:
:
:     CGMAT cycle number =     38
:
: function value    28.993898    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.23254929E-02
: Not converging with gamma equal   4.23254929E-02
: Trying gamma equal   4.44979668E-02
: Gamma decreased to   4.40634713E-02
:
:
: fvalues    0.0000000       28.993898       28.988565       28.993898    
:
:
:     CGMAT cycle number =     39
:
: function value    28.988565    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40634713E-02
: Gamma decreased to   4.36684750E-02
:
:
: fvalues    0.0000000       28.988565       28.983236       28.988565    
:
:
:     CGMAT cycle number =     40
:
: function value    28.983236    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:Bond angles  : refined atoms                     40     2.754     3.000
:Bond angles  : others                            24     0.651     3.000
:Chiral centres: refined atoms                     4     0.025     0.200
:Planar groups: refined atoms                     14     0.000     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             2     0.081     0.200
:VDW; torsion: refined_atoms                      12     0.243     0.200
:VDW; torsion.others                              12     0.075     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal   4.36684750E-02
: Gamma decreased to   4.33093868E-02
:
:
: fvalues    0.0000000       28.983236       28.977982       28.983236    
:
:    ****                        Final optimisation stage                        ****
:
:
:
:     CGMAT cycle number =      1
:
: function value    28.977982    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:Bond angles  : refined atoms                     40     2.753     3.000
:Bond angles  : others                            24     0.651     3.000
:Chiral centres: refined atoms                     4     0.025     0.200
:Planar groups: refined atoms                     14     0.000     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             2     0.081     0.200
:VDW; torsion: refined_atoms                      12     0.243     0.200
:VDW; torsion.others                              12     0.076     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.24999984E-02
: Gamma decreased to   4.19999994E-02
:
:
: fvalues    0.0000000       28.977982       28.973661       28.977982    
:
:
:     CGMAT cycle number =      2
:
: function value    28.973661    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.19999994E-02
: Gamma decreased to   3.24545428E-02
:
:
: fvalues    0.0000000       28.973661       28.968380       28.973661    
:
:
:     CGMAT cycle number =      3
:
: function value    28.968380    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.24545428E-02
: Not converging with gamma equal   3.24545428E-02
: Trying gamma equal   7.80123919E-02
: Gamma decreased to   6.89008236E-02
:
:
: fvalues    0.0000000       28.968380       28.965488       28.968380    
:
:
:     CGMAT cycle number =      4
:
: function value    28.965488    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.89008236E-02
: Gamma decreased to   6.06175810E-02
:
:
: fvalues    0.0000000       28.965488       28.962254       28.965488    
:
:
:     CGMAT cycle number =      5
:
: function value    28.962254    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.06175810E-02
: Gamma decreased to   5.30873574E-02
:
:
: fvalues    0.0000000       28.962254       28.958670       28.962254    
:
:
:     CGMAT cycle number =      6
:
: function value    28.958670    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.30873574E-02
: Gamma decreased to   4.62417006E-02
:
:
: fvalues    0.0000000       28.958670       28.954634       28.958670    
:
:
:     CGMAT cycle number =      7
:
: function value    28.954634    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.62417006E-02
: Gamma decreased to   4.00183760E-02
:
:
: fvalues    0.0000000       28.954634       28.950089       28.954634    
:
:
:     CGMAT cycle number =      8
:
: function value    28.950089    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.00183760E-02
: Not converging with gamma equal   4.00183760E-02
: Trying gamma equal   6.97205961E-02
: Gamma decreased to   6.37801513E-02
:
:
: fvalues    0.0000000       28.950089       28.947037       28.950089    
:
:
:     CGMAT cycle number =      9
:
: function value    28.947037    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.37801513E-02
: Gamma decreased to   5.83797470E-02
:
:
: fvalues    0.0000000       28.947037       28.943735       28.947037    
:
:
:     CGMAT cycle number =     10
:
: function value    28.943735    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.83797470E-02
: Gamma decreased to   5.34702875E-02
:
:
: fvalues    0.0000000       28.943735       28.940212       28.943735    
:
:
:     CGMAT cycle number =     11
:
: function value    28.940212    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.34702875E-02
: Gamma decreased to   4.90071438E-02
:
:
: fvalues    0.0000000       28.940212       28.936430       28.940212    
:
:
:     CGMAT cycle number =     12
:
: function value    28.936430    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.90071438E-02
: Gamma decreased to   4.49497402E-02
:
:
: fvalues    0.0000000       28.936430       28.932369       28.936430    
:
:
:     CGMAT cycle number =     13
:
: function value    28.932369    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.49497402E-02
: Gamma decreased to   4.12611924E-02
:
:
: fvalues    0.0000000       28.932369       28.928024       28.932369    
:
:
:     CGMAT cycle number =     14
:
: function value    28.928024    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.12611924E-02
: Not converging with gamma equal   4.12611924E-02
: Trying gamma equal   5.88656291E-02
: Gamma decreased to   5.53447418E-02
:
:
: fvalues    0.0000000       28.928024       28.924654       28.928024    
:
:
:     CGMAT cycle number =     15
:
: function value    28.924654    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.53447418E-02
: Gamma decreased to   5.21439351E-02
:
:
: fvalues    0.0000000       28.924654       28.921169       28.924654    
:
:
:     CGMAT cycle number =     16
:
: function value    28.921169    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.21439351E-02
: Gamma decreased to   4.92341109E-02
:
:
: fvalues    0.0000000       28.921169       28.917494       28.921169    
:
:
:     CGMAT cycle number =     17
:
: function value    28.917494    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.92341109E-02
: Gamma decreased to   4.65888157E-02
:
:
: fvalues    0.0000000       28.917494       28.913664       28.917494    
:
:
:     CGMAT cycle number =     18
:
: function value    28.913664    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.65888157E-02
: Gamma decreased to   4.41840030E-02
:
:
: fvalues    0.0000000       28.913664       28.909664       28.913664    
:
:
:     CGMAT cycle number =     19
:
: function value    28.909664    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.41840030E-02
: Gamma decreased to   4.19978090E-02
:
:
: fvalues    0.0000000       28.909664       28.905521       28.909664    
:
:
:     CGMAT cycle number =     20
:
: function value    28.905521    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.19978090E-02
: Not converging with gamma equal   4.19978090E-02
: Trying gamma equal   5.24319150E-02
: Gamma decreased to   5.03450930E-02
:
:
: fvalues    0.0000000       28.905521       28.902020       28.905521    
:
:
:     CGMAT cycle number =     21
:
: function value    28.902020    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.03450930E-02
: Gamma decreased to   4.84479815E-02
:
:
: fvalues    0.0000000       28.902020       28.898426       28.902020    
:
:
:     CGMAT cycle number =     22
:
: function value    28.898426    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.84479815E-02
: Gamma decreased to   4.67233360E-02
:
:
: fvalues    0.0000000       28.898426       28.894768       28.898426    
:
:
:     CGMAT cycle number =     23
:
: function value    28.894768    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.67233360E-02
: Gamma decreased to   4.51554768E-02
:
:
: fvalues    0.0000000       28.894768       28.891022       28.894768    
:
:
:     CGMAT cycle number =     24
:
: function value    28.891022    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.51554768E-02
: Not converging with gamma equal   4.51554768E-02
: Trying gamma equal   5.26384413E-02
: Gamma decreased to   5.11418469E-02
:
:
: fvalues    0.0000000       28.891022       28.887703       28.891022    
:
:
:     CGMAT cycle number =     25
:
: function value    28.887703    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.11418469E-02
: Gamma decreased to   4.97813076E-02
:
:
: fvalues    0.0000000       28.887703       28.884359       28.887703    
:
:
:     CGMAT cycle number =     26
:
: function value    28.884359    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.97813076E-02
: Gamma decreased to   4.85444553E-02
:
:
: fvalues    0.0000000       28.884359       28.880930       28.884359    
:
:
:     CGMAT cycle number =     27
:
: function value    28.880930    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.85444553E-02
: Gamma decreased to   4.74200435E-02
:
:
: fvalues    0.0000000       28.880930       28.877552       28.880930    
:
:
:     CGMAT cycle number =     28
:
: function value    28.877552    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.74200435E-02
: Gamma decreased to   4.63978499E-02
:
:
: fvalues    0.0000000       28.877552       28.874088       28.877552    
:
:
:     CGMAT cycle number =     29
:
: function value    28.874088    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.63978499E-02
: Not converging with gamma equal   4.63978499E-02
: Trying gamma equal   5.12764975E-02
: Gamma decreased to   5.03007695E-02
:
:
: fvalues    0.0000000       28.874088       28.870937       28.874088    
:
:
:     CGMAT cycle number =     30
:
: function value    28.870937    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.03007695E-02
: Gamma decreased to   4.94137406E-02
:
:
: fvalues    0.0000000       28.870937       28.867744       28.870937    
:
:
:     CGMAT cycle number =     31
:
: function value    28.867744    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.94137406E-02
: Gamma decreased to   4.86073531E-02
:
:
: fvalues    0.0000000       28.867744       28.864532       28.867744    
:
:
:     CGMAT cycle number =     32
:
: function value    28.864532    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.86073531E-02
: Gamma decreased to   4.78742719E-02
:
:
: fvalues    0.0000000       28.864532       28.861330       28.864532    
:
:
:     CGMAT cycle number =     33
:
: function value    28.861330    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.78742719E-02
: Gamma decreased to   4.72078361E-02
:
:
: fvalues    0.0000000       28.861330       28.858130       28.861330    
:
:
:     CGMAT cycle number =     34
:
: function value    28.858130    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.72078361E-02
: Not converging with gamma equal   4.72078361E-02
: Trying gamma equal   5.03885560E-02
: Gamma decreased to   4.97524105E-02
:
:
: fvalues    0.0000000       28.858130       28.855083       28.858130    
:
:
:     CGMAT cycle number =     35
:
: function value    28.855083    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.97524105E-02
: Gamma decreased to   4.91740964E-02
:
:
: fvalues    0.0000000       28.855083       28.852051       28.855083    
:
:
:     CGMAT cycle number =     36
:
: function value    28.852051    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.91740964E-02
: Gamma decreased to   4.86483574E-02
:
:
: fvalues    0.0000000       28.852051       28.849003       28.852051    
:
:
:     CGMAT cycle number =     37
:
: function value    28.849003    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.86483574E-02
: Gamma decreased to   4.81704138E-02
:
:
: fvalues    0.0000000       28.849003       28.845972       28.849003    
:
:
:     CGMAT cycle number =     38
:
: function value    28.845972    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.81704138E-02
: Not converging with gamma equal   4.81704138E-02
: Trying gamma equal   5.04515134E-02
: Gamma decreased to   4.99952920E-02
:
:
: fvalues    0.0000000       28.845972       28.843063       28.845972    
:
:
:     CGMAT cycle number =     39
:
: function value    28.843063    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.99952920E-02
: Gamma decreased to   4.95805480E-02
:
:
: fvalues    0.0000000       28.843063       28.840176       28.843063    
:
:
:     CGMAT cycle number =     40
:
: function value    28.840176    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           10     0.000     0.020
:Bond angles  : refined atoms                     40     2.740     3.000
:Bond angles  : others                            24     0.651     3.000
:Chiral centres: refined atoms                     4     0.024     0.200
:Planar groups: refined atoms                     14     0.000     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             2     0.081     0.200
:VDW; torsion: refined_atoms                      14     0.225     0.200
:VDW; torsion.others                              12     0.077     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal   4.95805480E-02
: Gamma decreased to   4.92035076E-02
:
:
: fvalues    0.0000000       28.840176       28.837288       28.840176    
: chir_max =  4.13386822E-02
: rms =  0.35088748    
: angle =  0.91783828    
:  Time in seconds: CPU =         0.55
:             Elapsed =           0.00
:
:    ****           Things for loggraph, R factor and others vs cycle            ****
:
:
:$TABLE: Rfactor analysis, stats vs cycle  :
:$GRAPHS: vs cycle :N:1,2,3:
::FOM vs cycle :N:1,4:
::-LL vs cycle :N:1,5:
::-LLfree vs cycle :N:1,6:
::Geometry vs cycle:N:1,7,8,9,10,11:
:$$
:    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
:$$
:       0   0.0      0.0      0.0             0.       0.0   0.0304  1.521   4.292  1.431   0.186
:       1   0.0      0.0      0.0             0.       0.0   0.0097  0.483   3.122  1.041   0.030
:       2   0.0      0.0      0.0             0.       0.0   0.0072  0.358   3.050  1.017   0.030
:       3   0.0      0.0      0.0             0.       0.0   0.0071  0.356   3.020  1.007   0.032
:       4   0.0      0.0      0.0             0.       0.0   0.0071  0.356   2.995  0.998   0.033
:       5   0.0      0.0      0.0             0.       0.0   0.0071  0.355   2.985  0.995   0.032
:       6   0.0      0.0      0.0             0.       0.0   0.0071  0.355   2.981  0.994   0.032
:       7   0.0      0.0      0.0             0.       0.0   0.0071  0.355   2.976  0.992   0.032
:       8   0.0      0.0      0.0             0.       0.0   0.0071  0.355   2.971  0.990   0.032
:       9   0.0      0.0      0.0             0.       0.0   0.0071  0.355   2.967  0.989   0.032
:      10   0.0      0.0      0.0             0.       0.0   0.0071  0.355   2.962  0.987   0.032
:      11   0.0      0.0      0.0             0.       0.0   0.0071  0.355   2.957  0.986   0.032
:      12   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.951  0.984   0.032
:      13   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.946  0.982   0.032
:      14   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.941  0.980   0.031
:      15   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.935  0.978   0.031
:      16   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.930  0.977   0.031
:      17   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.926  0.975   0.031
:      18   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.921  0.974   0.031
:      19   0.0      0.0      0.0             0.       0.0   0.0071  0.354   2.917  0.972   0.031
:      20   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.912  0.971   0.030
:      21   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.908  0.969   0.030
:      22   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.903  0.968   0.030
:      23   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.899  0.966   0.030
:      24   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.895  0.965   0.030
:      25   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.891  0.964   0.030
:      26   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.888  0.963   0.030
:      27   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.884  0.961   0.029
:      28   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.880  0.960   0.029
:      29   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.877  0.959   0.029
:      30   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.873  0.958   0.029
:      31   0.0      0.0      0.0             0.       0.0   0.0071  0.353   2.870  0.957   0.029
:      32   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.867  0.956   0.029
:      33   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.864  0.955   0.029
:      34   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.861  0.954   0.029
:      35   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.858  0.953   0.029
:      36   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.855  0.952   0.028
:      37   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.852  0.951   0.028
:      38   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.849  0.950   0.028
:      39   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.846  0.949   0.028
:      40   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.844  0.948   0.028
:      41   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.842  0.947   0.028
:      42   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.841  0.947   0.028
:      43   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.839  0.946   0.028
:      44   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.837  0.946   0.028
:      45   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.835  0.945   0.028
:      46   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.833  0.944   0.028
:      47   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.831  0.944   0.028
:      48   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.829  0.943   0.028
:      49   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.828  0.943   0.028
:      50   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.826  0.942   0.028
:      51   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.824  0.941   0.028
:      52   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.822  0.941   0.027
:      53   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.820  0.940   0.027
:      54   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.818  0.939   0.027
:      55   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.817  0.939   0.027
:      56   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.815  0.938   0.027
:      57   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.813  0.938   0.027
:      58   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.812  0.937   0.027
:      59   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.810  0.937   0.027
:      60   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.808  0.936   0.027
:      61   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.807  0.936   0.027
:      62   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.805  0.935   0.027
:      63   0.0      0.0      0.0             0.       0.0   0.0070  0.352   2.804  0.935   0.027
:      64   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.802  0.934   0.027
:      65   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.801  0.934   0.027
:      66   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.799  0.933   0.027
:      67   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.798  0.933   0.027
:      68   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.796  0.932   0.027
:      69   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.795  0.932   0.027
:      70   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.794  0.931   0.027
:      71   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.792  0.931   0.026
:      72   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.791  0.930   0.026
:      73   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.790  0.930   0.026
:      74   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.789  0.930   0.026
:      75   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.787  0.929   0.026
:      76   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.786  0.929   0.026
:      77   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.785  0.928   0.026
:      78   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.784  0.928   0.026
:      79   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.783  0.928   0.026
:      80   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.781  0.927   0.026
:      81   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.780  0.927   0.026
:      82   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.779  0.926   0.026
:      83   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.779  0.926   0.026
:      84   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.778  0.926   0.026
:      85   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.777  0.926   0.026
:      86   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.776  0.925   0.026
:      87   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.775  0.925   0.026
:      88   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.775  0.925   0.026
:      89   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.774  0.925   0.026
:      90   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.773  0.924   0.026
:      91   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.772  0.924   0.026
:      92   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.772  0.924   0.026
:      93   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.771  0.924   0.026
:      94   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.770  0.923   0.026
:      95   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.769  0.923   0.026
:      96   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.769  0.923   0.026
:      97   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.768  0.923   0.026
:      98   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.767  0.922   0.026
:      99   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.766  0.922   0.026
:     100   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.765  0.922   0.026
:     101   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.765  0.922   0.026
:     102   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.764  0.921   0.025
:     103   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.763  0.921   0.025
:     104   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.763  0.921   0.025
:     105   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.762  0.921   0.025
:     106   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.761  0.920   0.025
:     107   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.761  0.920   0.025
:     108   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.760  0.920   0.025
:     109   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.759  0.920   0.025
:     110   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.759  0.920   0.025
:     111   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.758  0.919   0.025
:     112   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.757  0.919   0.025
:     113   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.757  0.919   0.025
:     114   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.756  0.919   0.025
:     115   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.756  0.919   0.025
:     116   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.755  0.918   0.025
:     117   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.755  0.918   0.025
:     118   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.754  0.918   0.025
:     119   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.754  0.918   0.025
:     120   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.753  0.918   0.025
:     121   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.753  0.918   0.025
:     122   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.752  0.917   0.025
:     123   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.752  0.917   0.025
:     124   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.751  0.917   0.025
:     125   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.751  0.917   0.025
:     126   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.751  0.917   0.025
:     127   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.750  0.917   0.025
:     128   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.750  0.917   0.025
:     129   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.750  0.917   0.025
:     130   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.749  0.916   0.025
:     131   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.749  0.916   0.025
:     132   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.748  0.916   0.025
:     133   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.748  0.916   0.025
:     134   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.748  0.916   0.025
:     135   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.747  0.916   0.025
:     136   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.747  0.916   0.025
:     137   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.747  0.916   0.025
:     138   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.746  0.915   0.025
:     139   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.746  0.915   0.025
:     140   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.746  0.915   0.025
:     141   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.745  0.915   0.025
:     142   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.745  0.915   0.025
:     143   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.744  0.915   0.025
:     144   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.744  0.915   0.025
:     145   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.744  0.915   0.025
:     146   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.744  0.915   0.025
:     147   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.743  0.914   0.025
:     148   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.743  0.914   0.025
:     149   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.743  0.914   0.024
:     150   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.742  0.914   0.024
:     151   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.742  0.914   0.024
:     152   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.742  0.914   0.024
:     153   0.0      0.0      0.0             0.     INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 99 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "3GP"
There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/3/3GP.cif
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:48:41_2015_modification_0.pdb.gz
There are 2 data in coot-ccp4/libcheck_3GP.cif
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:48:41_2015_modification_1.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb
 PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 100 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb
 PDB file /home/emsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 101 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb
 PDB file /home/emsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 102 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "LIG"
There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LIG.cif
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:48:41_2015_modification_2.pdb.gz
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb
 PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 103 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
 PDB file /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 0/113
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 0/117
  INFO:: fill_ghost_info Constructed 6 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain A"
      Ghost 1 name: "NCS found from matching Chain E onto Chain A"
      Ghost 2 name: "NCS found from matching Chain G onto Chain A"
      Ghost 3 name: "NCS found from matching Chain D onto Chain B"
      Ghost 4 name: "NCS found from matching Chain F onto Chain B"
      Ghost 5 name: "NCS found from matching Chain H onto Chain B"
Molecule 109 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making conventional map from MTZ filename /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.145 seconds to read MTZ file
INFO:: 0.103 seconds to initialize map
INFO:: 0.077 seconds for FFT
INFO:: 0.014 seconds for statistics
      Map mean: ........ -8.79e-07
      Map sigma: ....... 0.1712
      Map maximum: ..... 1.343
      Map minimum: ..... -0.6954
INFO:: 0.009 seconds for contour map
INFO:: 0.348 seconds in total
INFO:: making difference map from MTZ filename /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.085 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.078 seconds for FFT
INFO:: 0.014 seconds for statistics
      Map mean: ........ 2.094e-06
      Map sigma: ....... 0.03339
      Map maximum: ..... 0.3661
      Map minimum: ..... -0.1917
INFO:: 0.004 seconds for contour map
INFO:: 0.182 seconds in total
Executing ligand search...
INFO:: ligand number 0 is molecule number 103   with wiggly flag: 0
ligand eigen values: 1.924  25.09  59.33  
 ligand eigen vectors: 
|   -0.4263,    0.8296,   -0.3606|
|   -0.1625,     0.322,    0.9327|
|    0.8899,    0.4562, -0.002469|
INFO:: Protein centre at: xyz = (     58.29,     34.65,     30.63)
Map statistics: mean: -0.02167 st.d: 0.08863
Map statistics: min: -0.6954, max: 0.7542
   -0.6773    6
   -0.6411    8
   -0.6048    27
   -0.5686    116
   -0.5324    354
   -0.4961    977
   -0.4599    1943
   -0.4236    3356
   -0.3874    5156
   -0.3511    6576
   -0.3149    7850
   -0.2787    8875
   -0.2424    9742
   -0.2062    11742
   -0.1699    16950
   -0.1337    29805
  -0.09746    58214
  -0.06122    102890
  -0.02498    142998
   0.01126    471775
    0.0475    106846
   0.08375    56087
      0.12    21597
    0.1562    6911
    0.1925    2135
    0.2287    920
     0.265    467
    0.3012    346
    0.3374    216
    0.3737    118
    0.4099    117
    0.4462    80
    0.4824    50
    0.5186    28
    0.5549    33
    0.5911    15
    0.6274    14
    0.6636    11
    0.6998    2
    0.7361    7
    0.7723    0
INFO:: find_clusters map_rms is 0.1711
INFO:: Using density cut-off: 0.1711 (1 sigma)  (mean -0.02168 stdev: 0.08862)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
There are 487 clusers
Here are the top 10 clusers:
  Number: 0 # grid points: 114 score: 39.72     
|  0.002711,   -0.8301,    0.5576|
|    0.6324,   -0.4305,    -0.644|
|    0.7746,    0.3544,    0.5238|
(     10.22,     41.14,     18.33)   xyz = (     1.249,     1.289,     1.099) eigenvalues: 36.16 84.69 384.3 
  Number: 1 # grid points: 70 score: 16.57     
|   -0.4748,     -0.44,   -0.7622|
|   -0.8071,   -0.1276,    0.5765|
|   -0.3509,    0.8889,   -0.2946|
(     36.54,     43.69,     42.89)   xyz = (    0.9048,    0.7209,     1.257) eigenvalues: 30.47 130.4 43.36 
  Number: 2 # grid points: 61 score: 15.17     
|    0.7705,   -0.1438,     0.621|
|    0.5329,    0.6798,   -0.5038|
|   -0.3497,    0.7191,    0.6005|
(     43.01,     6.792,     48.32)   xyz = (     1.124,    0.9864,     1.129) eigenvalues: 12.41 22.17 179.6 
  Number: 3 # grid points: 38 score: 13.42     
|   -0.6008,    0.4916,    0.6304|
|    0.7975,    0.3146,    0.5148|
|   0.05474,     0.812,    -0.581|
(     43.41,     22.55,     50.71)   xyz = (    0.8263,    0.6495,     1.179) eigenvalues: 8.316 73.33 13.15 
  Number: 4 # grid points: 36 score: 13.4     
|   -0.8278,   -0.4676,      0.31|
|   -0.5603,    0.6618,    -0.498|
|   0.02776,    -0.586,   -0.8099|
(     2.361,     56.41,     25.04)   xyz = (    0.6151,    0.6609,    0.6501) eigenvalues: 11.57 20.57 12.41 
  Number: 5 # grid points: 40 score: 12.47     
|    0.3772,    0.6453,    0.6643|
|    0.9261,   -0.2552,   -0.2779|
| -0.009792,      0.72,   -0.6939|
(     46.97,     1.923,     47.25)   xyz = (    0.9152,    0.5897,    0.9478) eigenvalues: 9.792 13.94 59.61 
  Number: 6 # grid points: 34 score: 12.37     
|   -0.3425,   -0.4238,    0.8385|
|   -0.9394,    0.1382,   -0.3139|
|   0.01716,   -0.8952,   -0.4454|
(     73.14,     32.61,     45.23)   xyz = (    0.7746,    0.5559,    0.6475) eigenvalues: 8.912 11.71 24.54 
  Number: 7 # grid points: 40 score: 11.81     
|   -0.6826,    0.6985,    0.2147|
|   -0.6946,   -0.7115,    0.1066|
|    0.2272,  -0.07637,    0.9708|
(     15.51,     51.69,     27.48)   xyz = (     1.045,      1.06,    0.5268) eigenvalues: 8.098 80.81 10.83 
  Number: 8 # grid points: 43 score: 11.61     
|   -0.4261,    0.4445,   -0.7879|
|   -0.8865,   -0.3791,    0.2655|
|   -0.1806,    0.8116,    0.5556|
(     27.27,      53.9,     17.59)   xyz = (     1.027,    0.5894,    0.8771) eigenvalues: 9.657 19.81 63.88 
debug:: n_ligands_for_cluster() top_score 4.042 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.007 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.092 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.857 and 3 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.387 and 4 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.611 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.1 and 2 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.691 and 2 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.123 and 2 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.841 and 5 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 136 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:48:53_2015_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:48:53_2015_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:48:53_2015_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sat_Sep__5_04:48:53_2015_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/dipole-residues.pdb
 PDB file /home/emsley/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 138 read successfully
DEBUG:: there were 0 types with no dictionary 
WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 139 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 139
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 139
INFO:: Reading coordinate file: /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb
 PDB file /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 140 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.016 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.069e-09
      Map sigma: ....... 0.3115
      Map maximum: ..... 2.978
      Map minimum: ..... -0.875
INFO:: 0.021 seconds for contour map
INFO:: 0.066 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 140

Sequence: ?EYTVITPGARTR
Confidence: 1

From    : HEYTVITPGARTR
Chain id: 0	Offset: 53
INFO:: backup file coot-backup/_home_emsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Sat_Sep__5_04:48:56_2015_modification_0.pdb.gz
bypassing ? at 0
Mutating to GLU at 1
Mutating poly_ala residue number 58
Mutating to TYR at 2
Mutating poly_ala residue number 59
Mutating to THR at 3
Mutating poly_ala residue number 60
Mutating to VAL at 4
Mutating poly_ala residue number 61
Mutating to ILE at 5
Mutating poly_ala residue number 62
Mutating to THR at 6
Mutating poly_ala residue number 63
Mutating to PRO at 7
Mutating poly_ala residue number 64
Mutating to GLY at 8
Mutating poly_ala residue number 65
Mutating to ALA at 9
Mutating poly_ala residue number 66
Mutating to ARG at 10
Mutating poly_ala residue number 67
Mutating to THR at 11
Mutating poly_ala residue number 68
Mutating to ARG at 12
Mutating poly_ala residue number 69
DEBUG:: Creating a new chain B
WARNING:: no rotamers probabilities for residue type GLY
INFO:: replace_coords: 9 atoms updated.
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
INFO:: replace_coords: 12 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 8 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
WARNING:: no rotamers probabilities for residue type GLY
WARNING:: no rotamers probabilities for residue type ALA
INFO:: replace_coords: 11 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 11 atoms updated.
INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.01207
    rms devi: 0.01345
    max devi: 0.02142
    min devi: 0.003856
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.2674
    rms devi: 0.3228
    max devi: 0.4951
    min devi: 0.1123
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.0847
INFO:: 5 matched atoms had: 
   mean devi: 0.2674
    rms devi: 0.3228
    max devi: 0.4952
    min devi: 0.1122
INFO:: 5 matched atoms had: 
   mean devi: 0.01198
    rms devi: 0.01335
    max devi: 0.02126
    min devi: 0.003873
INFO:: 5 matched atoms had: 
   mean devi: 0.0002426
    rms devi: 0.0002428
    max devi: 0.0002567
    min devi: 0.0002313
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.08456
INFO:: 5 matched atoms had: 
   mean devi: 0.2673
    rms devi: 0.3228
    max devi: 0.4951
    min devi: 0.1124
INFO:: 5 matched atoms had: 
   mean devi: 6.931e-05
    rms devi: 6.936e-05
    max devi: 7.334e-05
    min devi: 6.608e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.01203
    rms devi: 0.01341
    max devi: 0.02135
    min devi: 0.003862
INFO:: 5 matched atoms had: 
   mean devi: 0.0001386
    rms devi: 0.0001387
    max devi: 0.0001467
    min devi: 0.0001322
INFO:: 5 matched atoms had: 
   mean devi: 0.012
    rms devi: 0.01337
    max devi: 0.02129
    min devi: 0.003869
INFO:: 5 matched atoms had: 
   mean devi: 0.2674
    rms devi: 0.3228
    max devi: 0.4952
    min devi: 0.1122
INFO:: 5 matched atoms had: 
   mean devi: 0.2703
    rms devi: 0.3351
    max devi: 0.5361
    min devi: 0.08481
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Sat_Sep__5_04:48:57_2015_modification_0.pdb.gz
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: Matching/moving molecule number 144 to 144
ERROR:: No symmetry available
INFO:: LSQ matched 125 atoms
INFO:: 125 matched atoms had: 
   mean devi: 0.1419
    rms devi: 0.1486
    max devi: 0.2431
    min devi: 0.02832
INFO:: Axis orientation: (    0.3864,   -0.6781,   -0.6252)
INFO:: Rotation in CCP4 Polar Angles: Polar = (128.694,-60.3228,0.295209)
INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Sat_Sep__5_04:48:57_2015_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|         1,  0.003218, -0.003497|
| -0.003225,         1, -0.001985|
|  0.003491,  0.001997,         1|
(    -24.05,     -23.7,    -24.44)
No unit cell for this molecule, hence no fractional matrix.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/1wly.pdb
 PDB file /home/emsley/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 145 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/1yb5.pdb
 PDB file /home/emsley/data/greg-data/1yb5.pdb has been read.
Spacegroup: P 21 21 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 324/324
INFO:: NCS chain comparison 0/324
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 146 read successfully
DEBUG:: there were 2 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "CL"
There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CL.cif
INFO:: using standard CCP4 Refmac dictionary to search for "NAP"
There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/n/NAP.cif
INFO:: reference 145 has 750 atoms selected
INFO:: moving    146 has 842 atoms selected
superposing...
number of Ca atoms in selections: 110 (moving) and 100 (reference)
Another Go...

     Moving      Reference   Distance(/A)
      A   6
      A   7
      A   8  <--->  A   2  :  0.7510
      A   9  <--->  A   3  :  0.9422
      A  10  <--->  A   4  :  0.6300
      A  11  <--->  A   5  :  0.7119
      A  12  <--->  A   6  :  0.6310
      A  13  <--->  A   7  :  0.4675
      A  14  <--->  A   8  :  0.4264
      A  15  <--->  A   9  :  0.9792
      A  16  <--->  A  10  :  0.7549
      A  17  <--->  A  11  :  0.4884
      A  18  <--->  A  12  :  0.7451
      A  19  <--->  A  13  :  0.4606
      A  20  <--->  A  14  :  1.2809
      A  21  <--->  A  15  :  1.2412
      A  22  <--->  A  16  :  1.0733
      A  23  <--->  A  17  :  0.9730
      A  24  <--->  A  18  :  0.4705
      A  25  <--->  A  19  :  0.3560
      A  26  <--->  A  20  :  3.1145
      A  27
      A  28  <--->  A  21  :  1.5754
      A  29  <--->  A  22  :  1.6322
      A  30
      A  31  <--->  A  23  :  1.9973
      A  32  <--->  A  25  :  1.8324
      A  33  <--->  A  26  :  0.9310
      A  34  <--->  A  27  :  0.6808
      A  35  <--->  A  28  :  0.2674
      A  36  <--->  A  29  :  0.5995
      A  37  <--->  A  30  :  0.6992
      A  38  <--->  A  31  :  0.8620
      A  39  <--->  A  32  :  0.8421
      A  40  <--->  A  33  :  0.7208
      A  41  <--->  A  34  :  0.8681
      A  42  <--->  A  35  :  0.7781
      A  43  <--->  A  36  :  0.6211
      A  44  <--->  A  37  :  0.4657
      A  45  <--->  A  38  :  0.7475
      A  46  <--->  A  39  :  0.5170
      A  47  <--->  A  40  :  0.5058
      A  48  <--->  A  41  :  0.8897
      A  49  <--->  A  42  :  0.5835
      A  50  <--->  A  43  :  0.4347
      A  51  <--->  A  44  :  0.6192
      A  52  <--->  A  45  :  0.2150
      A  53  <--->  A  46  :  0.7474
      A  54  <--->  A  47  :  1.0213
      A  55  <--->  A  48  :  0.9208
      A  56  <--->  A  49  :  0.9392
      A  57
      A  58
      A  59
      A  60
      A  61
      A  62
      A  63
      A  64
      A  65  <--->  A  60  :  0.4666
      A  66  <--->  A  61  :  0.0523
      A  67  <--->  A  62  :  1.0719
      A  68  <--->  A  63  :  0.7933
      A  69  <--->  A  64  :  0.8916
      A  70  <--->  A  65  :  1.2580
      A  71  <--->  A  66  :  0.6932
      A  72  <--->  A  67  :  1.0345
      A  73  <--->  A  68  :  1.4417
      A  74  <--->  A  69  :  0.9092
      A  75  <--->  A  70  :  1.6166
      A  76  <--->  A  71  :  0.8741
      A  77  <--->  A  72  :  0.2388
      A  78  <--->  A  73  :  0.3118
      A  79  <--->  A  74  :  0.3887
      A  80  <--->  A  75  :  0.7613
      A  81  <--->  A  76  :  0.9044
      A  82  <--->  A  77  :  0.6090
      A  83  <--->  A  78  :  1.7978
      A  84  <--->  A  79  :  1.9256
      A  85  <--->  A  80  :  1.3416
      A  86  <--->  A  81  :  0.5658
      A  87  <--->  A  82  :  0.4480
      A  88  <--->  A  83  :  0.9078
      A  89  <--->  A  84  :  0.3625
      A  90  <--->  A  85  :  0.4040
      A  91  <--->  A  86  :  0.4586
      A  92  <--->  A  87  :  0.4340
      A  93  <--->  A  88  :  0.3664
      A  94  <--->  A  89  :  0.4921
      A  95  <--->  A  90  :  0.6498
      A  96  <--->  A  91  :  1.5805
      A  97  <--->  A  92  :  2.8839
      A  98
      A  99
      A 100

 Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG
 Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA

 Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY
 Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI

INFO:: backup file coot-backup/_home_emsley_data_greg-data_1yb5.pdb_Sat_Sep__5_04:48:59_2015_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|   -0.9117,   -0.3803,    0.1557|
|   -0.3625,    0.9227,     0.131|
|   -0.1935,   0.06299,   -0.9791|
(     70.65,     7.793,     21.29)
  Rotation - polar (omega,phi,kappa)  87.1413 101.0220 169.7385
  Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277
  Translation - Angstroms             70.6538 7.7930 21.2852 
INFO: core rmsd achieved: 1.0199 Angstroems
      number of residues in reference structure: 322
      number of residues in moving structure:    324
      number of residues in aligned sections (reference):  100
      number of residues in aligned sections (moving):     110
      number of aligned residues:  95
      number of gaps:              4
      number of misdirections:     0
      number of SSE combinations:  4.0000
      sequence identity:           30.5263%
WARNING:: Error reading /home/emsley/data/greg-data/1pyd.pdb
  0.0   0.0070  0.351   2.741  0.914   0.024
:     154   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.741  0.914   0.024
:     155   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.741  0.914   0.024
:     156   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.741  0.914   0.024
:     157   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.740  0.913   0.024
:     158   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.740  0.913   0.024
:     159   0.0      0.0      0.0             0.       0.0   0.0070  0.351   2.740  0.913   0.024
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:
: Refmac_5.8.0131:  End of Refmac_5.8.0131  
:Times: User:       4.5s System:    0.2s Elapsed:     0:04  
:
: : INFO:: libcheck-minimal? is #f PASS: Get monomer test Entered testcase - Set Bond thickness PASS: Set Bond thickness Entered testcase - Delete all-molecule Hydrogens here 1 PASS: Delete all-molecule Hydrogens Entered testcase - Non-Autoloads PASS: Non-Autoloads Entered testcase - Move and Refine Ligand test PASS: Move and Refine Ligand test Entered testcase - Many Molecules - Ligand Fitting Fitting NPO gave these results: # PASS: Many Molecules - Ligand Fitting Entered testcase - flip residue (around eigen vectors) distance: 4.05825923997285 distance d2: 4.95113364632015e-7 PASS: flip residue (around eigen vectors) Entered testcase - Test dipole info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0) PASS: Test dipole Entered testcase - Reading new dictionary restraints replaces PASS: Reading new dictionary restraints replaces Ended 03-ligand.scm Running 04-cootaneer.scm ... Entered testcase - Assignment of new PIR sequence overwrites old assignment debug seq: ("A" . "ACDEFGHIKLMNPQ") PASS: Assignment of new PIR sequence overwrites old assignment Entered testcase - Cootaneer Beta Strand Cootaneering: imol 140 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" PASS: Cootaneer Beta Strand Ended 04-cootaneer.scm Running 05-rna-ghosts.scm ... Entered testcase - RNA NCS Ghosts There are 8 residues in chain "A" There are 8 residues in chain "B" PASS: RNA NCS Ghosts Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example PASS: SSM - Frank von Delft's Example Entered testcase - SSM - Alice Dawson's Example 0 "/home/emsley/data/greg-data/tutorial-modern.pdb" 2 "/home/emsley/data/greg-data/ins-code-fragment-pre.pdb" 3 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 4 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 5 "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 6 "test-3hfl.map" 7 "/home/emsley/data/greg-data/tutorial-modern.pdb" 8 "mainchain" 9 "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 10 "atom selection from tutorial-add-terminal-1-test.pdb" 11 "/home/emsley/data/greg-data/frag-2wot.pdb" 12 "sphere selection from tutorial-modern.pdb" 14 "/home/emsley/data/greg-data/rotamer-test-fragment.pdb" 15 "/home/emsley/data/greg-data/res098.pdb" 16 "/home/emsley/data/greg-data/tutorial-modern.pdb" 17 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 18 "/home/emsley/data/greg-data/pdb3knw.ent" 19 "/home/emsley/data/greg-data/pdb1py3.ent" 22 "/home/emsley/data/greg-data/alt-conf-pepflip-test.pdb" 23 "/home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 24 "/home/emsley/data/greg-data/tutorial-modern.pdb" 25 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 26 "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 27 "/home/emsley/data/greg-data/tutorial-modern.pdb" 28 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 29 "/home/emsley/data/greg-data/alt-conf-waters.pdb" 30 "/home/emsley/data/greg-data/backrub-fragment.pdb" 31 "Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb" 32 "/home/emsley/data/greg-data/coords-B3A.pdb" 33 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 34 "/home/emsley/data/greg-data/test-TER-OXT.pdb" 35 "/home/emsley/data/greg-data/val.pdb" 36 "/home/emsley/data/greg-data/2yie-frag.pdb" 37 "/home/emsley/data/greg-data/4f8g.pdb" 38 "/home/emsley/data/greg-data/4f8g.pdb" 39 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 40 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 41 "/home/emsley/data/greg-data/tutorial-modern.pdb" 42 "Generic Masked Map" 43 "difference-map" 44 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 45 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 46 "averaged-map" 47 "difference-map" 48 "/home/emsley/data/greg-data/multi-carbo-coot-2.pdb" 49 "/home/emsley/data/greg-data/monomer-VAL.pdb" 50 "/home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 51 "atom selection from tutorial-modern.pdb" 52 "/home/emsley/data/greg-data/monomer-ACT.pdb" 53 "/home/emsley/data/greg-data/tutorial-modern.pdb" 54 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 55 "atom selection from tutorial-modern.pdb" 56 "/home/emsley/data/greg-data/tutorial-modern.pdb" 57 "/home/emsley/data/greg-data/tutorial-modern.pdb" 58 "/home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb" 59 "/home/emsley/data/greg-data/tutorial-modern.pdb" 60 "/home/emsley/data/greg-data/tutorial-modern.pdb" 61 "/home/emsley/data/greg-data/pdb3hfl.ent" 62 "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 63 "Ideal-A-form-RNA" 64 "Ideal-A-form-RNA" 65 "Ideal-A-form-DNA" 66 "Ideal-A-form-DNA" 67 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 68 "/home/emsley/data/greg-data/some-waters-with-ter.pdb" 69 "/home/emsley/data/greg-data/tm+some-waters.pdb" 70 "/home/emsley/data/greg-data/tutorial-modern.pdb" 71 "/home/emsley/data/greg-data/water-test-no-cell.pdb" 72 "/home/emsley/data/greg-data/pathological-water-test.pdb" 73 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 74 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 75 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 76 "/home/emsley/data/greg-data/tutorial-modern.pdb" 77 "/home/emsley/data/greg-data/pdb1hvv.ent" 78 "/home/emsley/data/greg-data/monomer-ACT.pdb" 79 "/home/emsley/data/greg-data/monomer-NPO.pdb" 80 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_77" 81 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 82 "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb" 83 "/home/emsley/data/greg-data/tutorial-modern.pdb" 84 "/home/emsley/data/greg-data/pdb1py3.ent" 85 "/home/emsley/data/greg-data/tutorial-modern.pdb" 86 "/home/emsley/data/greg-data/tutorial-modern.pdb" 87 "/home/emsley/data/greg-data/2goz-manip.pdb" 88 "/home/emsley/data/greg-data/HOF.RES" 89 "/home/emsley/data/greg-data/hollander.ins" 92 "/home/emsley/data/greg-data/insulin.fcf" 93 "atom selection from insulin.res" 94 "atom selection from insulin.res" 96 "/home/emsley/data/greg-data/horma-p21.res" 97 "new-horma.ins" 98 "/home/emsley/data/greg-data/crash.hat" 99 "coot-ccp4/monomer-3GP.pdb" 100 "/home/emsley/data/greg-data/monomer-3GP.pdb" 101 "/home/emsley/data/greg-data/test-LIG.pdb" 102 "/home/emsley/data/greg-data/test-LIG.pdb" 103 "/home/emsley/data/greg-data/monomer-NPO.pdb" 104 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" INFO:: Reading coordinate file: /home/emsley/data/greg-data/2qd9.pdb PDB file /home/emsley/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 147 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LGF" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LGF.cif INFO:: Reading coordinate file: /home/emsley/data/greg-data/2gtn.pdb PDB file /home/emsley/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 0/337 Molecule 148 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LIE" There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LIE.cif INFO:: reference 147 has 169 atoms selected INFO:: moving 148 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_home_emsley_data_greg-data_2gtn.pdb_Sat_Sep__5_04:49:01_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491 Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832 Translation - Angstroms 0.3207 0.6598 0.8819 INFO: core rmsd achieved: 0.2210 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1.0000 sequence identity: 100.0000% 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 149 read successfully INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0260 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0160 seconds for FFT INFO:: 0.0040 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0220 seconds for contour map INFO:: 0.0680 seconds in total INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.8760,16.1670,23.0330) B-factor: 20.0300 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.1788 rms devi: 4.8592 max devi: 46.2590 min devi: 0.1254 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: installing ghost map with name :Map 3 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 737280 out of 737280 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0003 st.d: 0.3250 Map statistics: min: -1.4894, max: 2.4019 -1.4407 3 -1.3435 7 -1.2462 16 -1.1489 7 -1.0516 17 -0.9543 61 -0.8570 255 -0.7598 907 -0.6625 3123 -0.5652 9819 -0.4679 26025 -0.3706 54787 -0.2733 87760 -0.1761 106865 -0.0788 105275 0.0185 88484 0.1158 67331 0.2131 50442 0.3103 38437 0.4076 28654 0.5049 21003 0.6022 15144 0.6995 10724 0.7968 7514 0.8940 5100 0.9913 3555 1.0886 2282 1.1859 1498 1.2832 914 1.3804 569 1.4777 316 1.5750 169 1.6723 84 1.7696 44 1.8669 35 1.9641 30 2.0614 9 2.1587 9 2.2560 2 2.3533 4 2.4506 0 INFO:: installing ghost map with name :Map 150 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0004 st.d: 0.3236 Map statistics: min: -1.4496, max: 2.3411 -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 2 2.3885 0 no diffs NCS target chain has 93 peers. INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 155 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:49:04_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:49:04_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:49:04_2015_modification_2.pdb.gz %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 155 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 155 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:49:04_2015_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:49:04_2015_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 155 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 155 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Sat_Sep__5_04:49:04_2015_modification_5.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1t6q.ent PDB file /home/emsley/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 156 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Sat_Sep__5_04:49:05_2015_modification_0.pdb.gz %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 156 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 156 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Sat_Sep__5_04:49:05_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Sat_Sep__5_04:49:05_2015_modification_2.pdb.gz INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 157 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 157 and chain_id: B %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 1 Checking chains for NCS matching to chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 540 in second selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.4989 rms devi: 2.7962 max devi: 6.6860 min devi: 0.4401 find_ncs_matrix returns (LSQ) | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) Adding ghost with name: NCS found from matching Chain A onto Chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.6728 rms devi: 2.9369 max devi: 6.1200 min devi: 0.2483 find_ncs_matrix returns (LSQ) | -0.3504, -0.8022, -0.4834| | -0.7587, -0.05952, 0.6488| | -0.5492, 0.594, -0.5878| ( -29.05, 14.61, -72.53) Adding ghost with name: NCS found from matching Chain C onto Chain B INFO:: NCS chain comparison 61/62 First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 1.7317 rms devi: 1.9769 max devi: 7.9453 min devi: 0.5297 find_ncs_matrix returns (LSQ) | -0.3815, -0.9208, -0.08098| | -0.9191, 0.3685, 0.1396| | -0.09874, 0.1277, -0.9869| ( -11.18, 4.757, -127.2) Adding ghost with name: NCS found from matching Chain D onto Chain B INFO:: NCS chain comparison 0/62 INFO:: set_ncs_master_chain Constructed 3 ghosts Ghost info:: NCS found from matching Chain A onto Chain B Ghost info:: NCS found from matching Chain C onto Chain B Ghost info:: NCS found from matching Chain D onto Chain B Symmetry available for this molecule INFO:: Matching/moving molecule number 158 to 157 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Sat_Sep__5_04:49:08_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) Symmetry available for this molecule INFO:: Matching/moving molecule number 159 to 157 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.1943 rms devi: 0.2112 max devi: 0.3583 min devi: 0.0329 INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095) INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Sat_Sep__5_04:49:08_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.6203, -0.2279, -0.7505| | -0.4559, -0.6739, 0.5814| | -0.6382, 0.7028, 0.3141| ( -22.14, -19.93, 1.626) INFO:: fractional coordinates matrix: | -0.8835, -0.09252, -0.543| | -0.5264, -0.4107, 0.8789| | -0.4875, 0.7087, 0.3141| ( -0.381, -0.2605, 0.01406) Symmetry available for this molecule INFO:: Matching/moving molecule number 160 to 157 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.4174 rms devi: 0.4531 max devi: 0.7926 min devi: 0.0759 INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411) INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Sat_Sep__5_04:49:08_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 161 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/emsley/data/greg-data/1hvv_sigmaa.mtz Number of OBSERVED reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.0400 seconds to read MTZ file INFO:: 0.0230 seconds to initialize map INFO:: 0.0270 seconds for FFT INFO:: 0.0040 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0100 seconds for contour map INFO:: 0.1040 seconds in total INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.4989 rms devi: 2.7962 max devi: 6.6860 min devi: 0.4401 find_ncs_matrix returns (LSQ) | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) INFO:: NCS chain comparison 66/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.9713 rms devi: 2.1729 max devi: 4.5411 min devi: 0.4295 find_ncs_matrix returns (LSQ) | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) INFO:: NCS chain comparison 61/67 First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600 First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.7042 rms devi: 4.0859 max devi: 9.4383 min devi: 0.2858 find_ncs_matrix returns (LSQ) | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 162 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5945 0.3997 3629 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 error (syntax error) error (syntax error) error (not syntax error) Traceback (most recent call last): File "", line 1, in NameError: name 'rr_not_found_thing' is not defined INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 171 read successfully DEBUG:: there were 0 types with no dictionary Entering test: OXT in restraints? INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/ There are 142 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/AR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HOH.cif There are 2 data in /home/emsley/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.1414 PASS: test symm trans to origin Entering test: test lsq plane LSQ deviations: 0.0000 0.0000 PASS: test lsq plane Entering test: test COO modification INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/ There are 142 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ALA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ASN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLN.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLY.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GLU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PHE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HIS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/i/ILE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LYS.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/l/LEU.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MET.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/m/MSE.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PRO.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/ARG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SER.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/THR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/v/VAL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TRP.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/t/TYR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/p/PO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/s/SO4.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GOL.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CIT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/AR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CR.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/CD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/GD.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/a/A.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/c/C.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/g/G.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/u/U.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DA.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DC.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DG.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/d/DT.cif There are 2 data in /home/emsley/ccp4/ccp4-6.5/ccp4-6.5/lib/data/monomers/h/HOH.cif INFO:: Reading coordinate file: /home/emsley/data/greg-data/hideous-OXT.pdb PDB file /home/emsley/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom created 7 bond restraints created 8 angle restraints created 1 plane restraints created 1 chiral vol restraints created 2 torsion restraints created 23 restraints INFO:: make_restraints(): made 20 non-bonded restraints initial distortion_score: 5677.4757 Initial RMS Z values bonds: 3.7208 angles: 7.4688 torsions: 0.2764 planes: 16.9011 non-bonded: 221.7967 chiral vol: 1.2266 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 895) at 21.2864 Final Estimated RMS Z Scores: bonds: 1.0044 angles: 0.8989 torsions: 0.0371 planes: 0.0012 non-bonded: 0.2566 chiral vol: 0.0046 rama plot: N/A start_pos: N/A GemanMcCl: N/A refinement_took 0.0210 seconds OXT out of plane distance: 0.0001 OXT->O distance: 2.2547 PASS: test COO modification Entering test: remove whitespace PASS: remove whitespace Entering test: New comp_ids are sane PASS: New comp_ids are sane Entering test: Residues for phi,psi are close enough to be considered linked INFO:: Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 bad residues for phi,psi calculation bad residues for phi,psi calculation PASS: Residues for phi,psi are close enough to be considered linked 105 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 106 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 107 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 108 "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb" 109 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 110 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 111 "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 112 "Masked (by protein)" 113 "Fitted ligand #0-0" 114 "Fitted ligand #0-1" 115 "Fitted ligand #0-2" 116 "Fitted ligand #1-0" 117 "Fitted ligand #1-1" 118 "Fitted ligand #2-0" 119 "Fitted ligand #2-1" 120 "Fitted ligand #2-2" 121 "Fitted ligand #2-3" 122 "Fitted ligand #3-0" 123 "Fitted ligand #3-1" 124 "Fitted ligand #3-2" 125 "Fitted ligand #4-0" 126 "Fitted ligand #5-0" 127 "Fitted ligand #5-1" 128 "Fitted ligand #6-0" 129 "Fitted ligand #6-1" 130 "Fitted ligand #7-0" 131 "Fitted ligand #8-0" 132 "Fitted ligand #8-1" 133 "Fitted ligand #9-0" 134 "Fitted ligand #9-1" 135 "Fitted ligand #9-2" 136 "coot-ccp4/monomer-3GP.pdb" 137 "Copy_of_coot-ccp4/monomer-3GP.pdb" 138 "/home/emsley/data/greg-data/dipole-residues.pdb" 139 "/home/emsley/data/greg-data/tutorial-modern.pdb" 140 "/home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb" 141 "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 142 "Ideal-A-form-RNA" 145 "/home/emsley/data/greg-data/1wly.pdb" 146 "/home/emsley/data/greg-data/1yb5.pdb" PASS: SSM - Alice Dawson's Example Entered testcase - SSM by atom selection [JED Example] PASS: SSM by atom selection [JED Example] Ended 06-ssm.scm Running 07-ncs.scm ... Entered testcase - NCS maps test PASS: NCS maps test Entered testcase - NCS chains info NCS info: (("A" "B")) PASS: NCS chains info Entered testcase - NCS deviation info PASS: NCS deviation info Entered testcase - NCS Residue Range copy PASS: NCS Residue Range copy Entered testcase - NCS Residue Range edit to all chains result: (#t #t) PASS: NCS Residue Range edit to all chains Entered testcase - Manual NCS ghosts generates correct NCS chain ids NCS ghost chain IDs pre: (("B" "A" "C" "D")) NCS ghost chain IDs post: (("B" "A" "C" "D")) PASS: Manual NCS ghosts generates correct NCS chain ids Entered testcase - NCS maps overwrite existing maps ==== test-name: "Map 162 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 162 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 162 NCS found from matching Chain D onto Chain A" n-matchers: 2 PASS: NCS maps overwrite existing maps Ended 07-ncs.scm Running 08-utils.scm ... Entered testcase - Test key symbols WARNING:: could not find key-sym-code for "missing key" PASS: Test key symbols Entered testcase - Test running a Python function test_val_2 passed test_val_3 passed PASS: Test running a Python function Entered testcase - Internal/External Molecule Numbers match PASS: Internal/External Molecule Numbers match Entered testcase - spacegroup operators to space group conversion PASS: spacegroup operators to space group conversion Ended 08-utils.scm Running 09-internal.scm ... Entered testcase - Test internal functions PASS: Test internal functions Ended 09-internal.scm === greg-tests Summary === # of testcases attempted 117 # of expected passes 117 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 Loading greg-tests/end.grg ... Loaded greg-tests/end.grg === Summary of all tests === # of tools 1 # of testcases attempted 117 # of expected passes 117 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 test_coot: coot test passed