testing with greg testing with greg currently we are here: /lmb/home/pemsley/autobuild/building/pcterm37.lmb.internal_2016-12-27__T04_00_02/test-tar/coot-Linux-x86_64-centos-5-pre-release-gtk2-python Tue Dec 27 04:21:52 GMT 2016 WARNING:: ccp4 setup file /home/emsley/ccp4/ccp4-6.2.0/include/ccp4.setup-sh does not exist. /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ INFO:: Reading coordinate file: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) INFO:: coot.py imported Running python script /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Morning Paul, Welcome to Coot version 0.8.8-pre (set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.8.8-pre") (use-graphics-interface-state) Running python script /lmb/home/pemsley/.coot-preferences/pepflip-new.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good morning Paul. Welcome to Coot 0.8.8-pre") (set-display-lists-for-maps 0) load /lmb/home/pemsley/.coot-preferences/angle-factor.scm (set-hardware-stereo-angle-factor 1.50) load /lmb/home/pemsley/.coot-preferences/coot-preferences.scm (set-filter-fileselection-filenames 0) (unset-sticky-sort-by-date) (set-colour-map-rotation-on-read-pdb 21.00) (set-colour-map-rotation-on-read-pdb-c-only-flag 1) (set-density-size 12.60) (set-swap-difference-map-colours 0) (set-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) load /lmb/home/pemsley/.coot-preferences/enhanced-ligand.scm load /lmb/home/pemsley/.coot-preferences/key-bindings.scm (set-add-terminal-residue-do-post-refine 1) (set-terminal-residue-do-rigid-body-refine 0) load /lmb/home/pemsley/.coot-preferences/template-key-bindings.scm (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run command-line-greg.scm INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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: /lmb/home/pemsley/data/greg-data/2WF6.cif mmCIF file /lmb/home/pemsley/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 in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb PDB file /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule 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/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Dec_27_04:21:53_2016_modification_0.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Dec_27_04:21:53_2016_modification_1.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Dec_27_04:21:53_2016_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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.056 seconds to read MTZ file INFO:: 0.03 seconds to initialize map INFO:: 0.036 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.97066e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.04 seconds for contour map INFO:: 0.169 seconds in total WARNING:: file xx-missing.mtz does not exist CCP4MTZfile: open_read - File missing or corrupted: /lmb/home/pemsley/data/greg-data/broken.mtz >>>>>> 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 <<<<<< INFO:: not an mtz file: /lmb/home/pemsley/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.046 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.97066e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.039 seconds for contour map INFO:: 0.128 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 80, 108, 108) INFO:: 0.041 seconds to read MTZ file INFO:: 0.016 seconds to initialize map INFO:: 0.029 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 7.76541e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.81878 Map minimum: ..... -1.02352 INFO:: 0.008 seconds for contour map INFO:: 0.102 seconds in total INFO:: map file type was determined to be CCP4 type INFO:: attempting to read CCP4 map: test-3hfl.map closing CCP4 map: test-3hfl.map Map statistics: mean: 7.76541e-11 st.d: 0.260405 Map statistics: min: -1.02352, max: 1.81878 -0.987993 5 -0.916935 16 -0.845877 73 -0.77482 214 -0.703762 683 -0.632705 1662 -0.561647 3458 -0.49059 6630 -0.419532 10974 -0.348475 16784 -0.277417 24050 -0.20636 35976 -0.135302 52684 -0.0642446 70826 0.00681294 75511 0.0778705 59049 0.148928 33738 0.219986 17844 0.291043 11108 0.362101 8875 0.433158 7682 0.504216 6862 0.575273 5661 0.646331 4738 0.717388 3751 0.788446 2781 0.859503 1898 0.930561 1313 1.00162 799 1.07268 428 1.14373 224 1.21479 120 1.28585 55 1.35691 44 1.42796 20 1.49902 9 1.57008 7 1.64114 4 1.71219 3 1.78325 1 1.85431 0 INFO:: n grid points: 466560 INFO:: mean before filtering: 7.76541e-11 INFO:: variance before filtering: 0.0678109 INFO:: filter by ignoring 364 of 466560 counts ( = 0.07802%) with values around -0.03426 from bin 3480 of 10000 Map mean: ........ 2.688e-05 Map rmsd: ........ 0.2604 Map maximum: ..... 1.819 Map minimum: ..... -1.024 WARNING:: Error reading . . is a directory. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. ERROR 42 READ: Duplicate sequence number and insertion code. LINE #868 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.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: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 1000 random trials --- in best_fit_phi_psi() with offset -1 INFO:: Fitting terminal residue without individual rigid body fitting. --- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000 called fit_terminal_residue_generic() residue-seqnum: 1 offset: -1 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:21:55_2016_modification_0.pdb.gz Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:21:55_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/frag-2wot.pdb PDB file /lmb/home/pemsley/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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_Tue_Dec_27_04:21:56_2016_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:21:56_2016_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:21:56_2016_modification_2.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb PDB file /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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: /lmb/home/pemsley/data/greg-data/res098.pdb PDB file /lmb/home/pemsley/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links 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 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 9 non-bonded restraints initial distortion_score: 26.65 Initial RMS Z values bonds: 0.2292 angles: 0.4339 torsions: N/A planes: 0.3222 non-bonded: 0 chiral vol: 0.1627 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 143) at 9.945 Final Estimated RMS Z Scores: bonds: 0.09509 angles: 0.6654 torsions: N/A planes: 0.649 non-bonded: 0 chiral vol: 0.5907 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 3.959 debug:: restraints results 1 5 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_res098.pdb_Tue_Dec_27_04:21:57_2016_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.049 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.04 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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:21:57_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:21:57_2016_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.93 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3knw.ent PDB file /lmb/home/pemsley/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links 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:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3knw.ent_Tue_Dec_27_04:21:57_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links 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 WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1py3.ent_Tue_Dec_27_04:21:58_2016_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 Good morning Paul Emsley PI Garib Murshudov added 28092012. Welcome to Coot 0.8.8-pre. === 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 0.311501026153564 #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 MSE Entered testcase - Hs are correctly swapped on a TYR bond-length-within-tolerance? bond-length 0.93069991132425 with target 0.93 and tolerance 0.02 for atom ((" CD1" "") (1.0 (22.3700008392334 0.288300007581711 0.351099997758865 0.210400000214577 0.0551000013947487 0.0124000003561378 0.00350000010803342) " C" "") (61.2610015869141 -13.2200002670288 1.25)) is ((" HD1" "") (1.0 22.7800006866455 " H" "") (61.4099998474121 -12.8690004348755 2.09899997711182)) bond-length-within-tolerance? bond-length 0.930136198469449 with target 0.93 and tolerance 0.02 for atom ((" CD2" "") (1.0 (24.4099998474121 0.258899986743927 0.405699998140335 0.262800008058548 0.0627999976277351 -0.0269000008702278 -0.00970000028610229) " C" "") (59.9500007629395 -13.3459997177124 -0.740000009536743)) is ((" HD2" "") (1.0 24.3099994659424 " H" "") (59.2050018310547 -13.0869998931885 -1.23300004005432)) bond-length-within-tolerance? bond-length 0.930888837109095 with target 0.93 and tolerance 0.02 for atom ((" CE1" "") (1.0 (22.1599998474121 0.280600011348724 0.314999997615814 0.246199995279312 0.0603000000119209 -0.0186000000685453 -0.0172000005841255) " C" "") (62.1650009155273 -14.1079998016357 0.726000010967255)) is ((" HE1" "") (1.0 22.1200008392334 " H" "") (62.9140014648438 -14.3520002365112 1.22200000286102)) bond-length-within-tolerance? bond-length 0.929591631283786 with target 0.93 and tolerance 0.02 for atom ((" CE2" "") (1.0 (23.9099998474121 0.281399995088577 0.359200000762939 0.267500013113022 0.0529999993741512 -0.0285000000149012 -0.0131999999284744) " C" "") (60.8559989929199 -14.2670001983643 -1.29900002479553)) is ((" HE2" "") (1.0 23.5400009155273 " H" "") (60.7249984741211 -14.6049995422363 -2.15499997138977)) INFO:: 25 residues had their atoms swapped INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.048 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.039 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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:21:58_2016_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: /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb PDB file /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-pepflip-test.pdb_Tue_Dec_27_04:21:58_2016_modification_0.pdb.gz flipped 65 A INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 0xb1d60e0 omega: 1 12.77 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:21:59_2016_modification_0.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:21:59_2016_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 flipped 11 A INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:21:59_2016_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 4 angle links 2 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 27 non-bonded restraints initial distortion_score: 4134 Initial RMS Z values bonds: 15.46 angles: 7.124 torsions: N/A planes: 2.181 non-bonded: 126.2 chiral vol: 3.045 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -4889 Final Estimated RMS Z Scores: bonds: 0.8851 angles: 0.7688 torsions: N/A planes: 2.525 non-bonded: 0.2186 chiral vol: 0.3847 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.913 Refinement elapsed time: 0.019 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:21:59_2016_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:21:59_2016_modification_4.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:21:59_2016_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.683 created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 4 angle links 2 plane links 1 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 7 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 63 non-bonded restraints initial distortion_score: -6042 Initial RMS Z values bonds: 0.9079 angles: 1.599 torsions: N/A planes: 3.041 non-bonded: 0.6111 chiral vol: 0.4155 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 98) at -6165 Final Estimated RMS Z Scores: bonds: 0.8707 angles: 0.7106 torsions: N/A planes: 2.58 non-bonded: 0.1002 chiral vol: 0.2221 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.056 Refinement elapsed time: 0.018 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:21:59_2016_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.048 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.038 seconds for contour map INFO:: 0.128 seconds in total created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 6 non-bonded restraints initial distortion_score: -2777 Initial RMS Z values bonds: 1.674 angles: 1.07 torsions: N/A planes: 0.6113 non-bonded: 9.246 chiral vol: 1.462 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 86) at -2900 Final Estimated RMS Z Scores: bonds: 1.073 angles: 1.21 torsions: N/A planes: 0.3785 non-bonded: 3.393 chiral vol: 0.7055 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.486 Refinement elapsed time: 0.009 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:21:59_2016_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:22:00_2016_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: created 81 restraints created 34 bond restraints created 39 angle restraints created 2 plane restraints created 6 chiral vol restraints Link restraints: 2 bond links 6 angle links 0 plane links 4 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 5 bond links 15 angle links 10 plane links 5 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 1311 non-bonded restraints initial distortion_score: -2.088e+04 Initial RMS Z values bonds: 1.743 angles: 1.268 torsions: N/A planes: 0.8383 non-bonded: 0.0008054 chiral vol: 0.8944 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 112) at -2.13e+04 Final Estimated RMS Z Scores: bonds: 1.13 angles: 0.7341 torsions: N/A planes: 0.6089 non-bonded: 0 chiral vol: 0.2766 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.027 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:22:00_2016_modification_1.pdb.gz INFO:: replace_coords: 39 atoms updated. INFO:: created 84 restraints created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints Link restraints: 4 bond links 12 angle links 8 plane links 3 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 1031 non-bonded restraints initial distortion_score: -7315 Initial RMS Z values bonds: 0.9807 angles: 1.018 torsions: N/A planes: 1.787 non-bonded: 6.405 chiral vol: 10.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 99) at -1.584e+04 Final Estimated RMS Z Scores: bonds: 1.985 angles: 1.867 torsions: N/A planes: 1.567 non-bonded: 0.06554 chiral vol: 1.817 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.395 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:22:00_2016_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.048 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.035 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.039 seconds for contour map INFO:: 0.13 seconds in total created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -6040 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 1.985 non-bonded: 11.39 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 113) at -1.167e+04 Final Estimated RMS Z Scores: bonds: 1.889 angles: 1.817 torsions: N/A planes: 2.003 non-bonded: 0.09339 chiral vol: 1.934 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.926 Refinement elapsed time: 0.095 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 1831 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 1.985 non-bonded: 11.39 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -3126 Final Estimated RMS Z Scores: bonds: 0.6814 angles: 0.8258 torsions: N/A planes: 1.69 non-bonded: 0.005352 chiral vol: 0.7937 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.206 Refinement elapsed time: 0.277 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb PDB file /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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/_lmb_home_pemsley_data_greg-data_alt-conf-waters.pdb_Tue_Dec_27_04:22:01_2016_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: /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb PDB file /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Tue_Dec_27_04:22:02_2016_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Tue_Dec_27_04:22:02_2016_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/coords-B3A.pdb PDB file /lmb/home/pemsley/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 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 24) at 4.458e-05 Final Estimated RMS Z Scores: bonds: 0.001074 angles: 0.002729 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.001253 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.061 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Tue_Dec_27_04:22:02_2016_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/lib-B3A.cif" not found. init_refmac_mon_lib /lmb/home/pemsley/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: 4.458e-05 Initial RMS Z values bonds: 0.001074 angles: 0.002729 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.001253 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 1) at 3.556e-05 Final Estimated RMS Z Scores: bonds: 0.0004138 angles: 0.002621 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0005972 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.294 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Tue_Dec_27_04:22:02_2016_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. 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: 3.018 Initial RMS Z values bonds: 0.6707 angles: 0.3754 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 16) at 2.335e-06 Final Estimated RMS Z Scores: bonds: 0.0004366 angles: 0.0005257 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 1.393e-07 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.529 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Tue_Dec_27_04:22:02_2016_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.048 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.038 seconds for FFT INFO:: 0.006 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.039 seconds for contour map INFO:: 0.132 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb PDB file /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 34 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_test-TER-OXT.pdb_Tue_Dec_27_04:22:03_2016_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: /lmb/home/pemsley/data/greg-data/val.pdb PDB file /lmb/home/pemsley/data/greg-data/val.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule 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/_lmb_home_pemsley_data_greg-data_val.pdb_Tue_Dec_27_04:22:03_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2yie-frag.pdb PDB file /lmb/home/pemsley/data/greg-data/2yie-frag.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2yie-frag.pdb_Tue_Dec_27_04:22:03_2016_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: /lmb/home/pemsley/data/greg-data/4f8g.pdb PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 37 read successfully DEBUG:: there were 1 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Tue_Dec_27_04:22:04_2016_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: /lmb/home/pemsley/data/greg-data/4f8g.pdb PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 38 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Tue_Dec_27_04:22:04_2016_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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.047 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.036 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.033 seconds for contour map INFO:: 0.125 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.048 seconds to read MTZ file INFO:: 0.051 seconds to initialize map INFO:: 0.054 seconds for FFT INFO:: 0.012 seconds for statistics Map mean: ........ 1.229e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.052 seconds for contour map INFO:: 0.217 seconds in total INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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: -0.001404 st.d: 0.3055 Map statistics: min: -0.8957, max: 2.764 -0.85 7 -0.7585 47 -0.667 345 -0.5755 1966 -0.484 7547 -0.3926 21145 -0.3011 36984 -0.2096 49747 -0.1181 62502 -0.02661 78146 0.06488 56227 0.1564 31741 0.2479 15372 0.3393 9396 0.4308 7278 0.5223 6354 0.6138 5287 0.7053 4622 0.7968 3865 0.8883 3168 0.9798 2366 1.071 1769 1.163 1258 1.254 879 1.346 637 1.437 417 1.529 237 1.62 135 1.712 69 1.803 46 1.895 18 1.986 8 2.078 2 2.169 6 2.261 2 2.352 0 2.444 1 2.535 3 2.627 0 2.718 1 2.81 0 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=0.2271131687677 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.28867626569884 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 1.889" 1.88942098617554) ("Angles" "Angles: 1.817" 1.81723749637604) ("Planes" "Planes: 2.003" 2.00255990028381) ("Non-bonded" "Non-bonded: 0.306" 0.305593401193619) ("Chirals" "Chirals: 1.934" 1.93418478965759))) ow factor: 1.91085079312325 INFO:: setting refinement weight to 16.4322750809894 refinement results: ("" 0 (("Bonds" "Bonds: 0.681" 0.681407988071442) ("Angles" "Angles: 0.826" 0.825836062431335) ("Planes" "Planes: 1.690" 1.68959844112396) ("Non-bonded" "Non-bonded: 0.073" 0.0731583088636398) ("Chirals" "Chirals: 0.794" 0.793652057647705))) ow factor: 0.997623637318611 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: (0.966407835483551 0.928917765617371 0.952126264572144 0.646193742752075 0.637681484222412 0.801941633224487 0.734838247299194 1.07139241695404 0.994847416877747 0.931116223335266 0.788039326667786) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) Map statistics: mean: -0.001364 st.d: 0.06029 Map statistics: min: -2.977, max: 0.7461 -2.931 1 -2.838 1 -2.744 1 -2.651 2 -2.558 2 -2.465 0 -2.372 2 -2.279 1 -2.186 1 -2.093 4 -2 2 -1.907 3 -1.814 4 -1.721 4 -1.627 8 -1.534 11 -1.441 15 -1.348 33 -1.255 33 -1.162 49 -1.069 65 -0.9759 120 -0.8828 145 -0.7898 159 -0.6967 202 -0.6036 249 -0.5105 275 -0.4174 291 -0.3243 411 -0.2313 440 -0.1382 581 -0.0451 300768 0.04798 101975 0.1411 1213 0.2341 1098 0.3272 767 0.4203 463 0.5134 156 0.6065 36 0.6995 9 0.7926 0 diff-high-values: (0.00350912800058722 -6.19740807451308e-4 0.00425341492518783 0.00702535035088658 0.00246789562515914 0.00335022434592247 0.00518704112619162 0.00365045410580933 0.00318347150459886 0.00567072723060846 0.00321402191184461) diff-low-values: (-0.869144380092621 -0.882691860198975 -1.18596029281616 -1.16333603858948 -1.04177522659302 -0.848253965377808 -0.827702522277832 -0.704876363277435 -0.93985915184021 -0.53272557258606) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 44 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.048 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.038 seconds for contour map INFO:: 0.128 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.048 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.034 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 8.971e-10 Map sigma: ....... 0.3115 Map maximum: ..... 3.014 Map minimum: ..... -0.8957 INFO:: 0.039 seconds for contour map INFO:: 0.129 seconds in total INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.047 seconds to read MTZ file INFO:: 0.071 seconds to initialize map INFO:: 0.07 seconds for FFT INFO:: 0.019 seconds for statistics Map mean: ........ 1.161e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.071 Map minimum: ..... -0.8775 INFO:: 0.085 seconds for contour map INFO:: 0.292 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 128, 160, 80) by 1 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1 Map statistics: mean: 1.687e-07 st.d: 0.3111 Map statistics: min: -0.8941, max: 3.007 -0.8453 8 -0.7478 64 -0.6503 542 -0.5527 3067 -0.4552 12045 -0.3577 29986 -0.2601 46658 -0.1626 61563 -0.06508 73639 0.03245 68489 0.13 41912 0.2275 19494 0.325 11050 0.4226 8221 0.5201 7074 0.6176 5839 0.7152 5071 0.8127 4183 0.9102 3295 1.008 2384 1.105 1722 1.203 1175 1.3 843 1.398 560 1.495 325 1.593 179 1.69 90 1.788 59 1.886 23 1.983 9 2.081 8 2.178 6 2.276 2 2.373 2 2.471 4 2.568 3 2.666 2 2.763 2 2.861 1 2.958 0 3.056 1 Map statistics: mean: -1.678e-07 st.d: 0.001076 Map statistics: min: -0.01094, max: 0.0109 -0.01067 1 -0.01012 1 -0.009578 0 -0.009032 1 -0.008485 3 -0.007939 2 -0.007393 4 -0.006847 7 -0.006301 25 -0.005755 37 -0.005208 103 -0.004662 260 -0.004116 640 -0.00357 1269 -0.003024 2611 -0.002478 5434 -0.001931 10529 -0.001385 21798 -0.0008391 51978 -0.000293 109494 0.0002532 110466 0.0007994 52014 0.001346 20447 0.001892 9607 0.002438 5235 0.002984 2974 0.00353 1857 0.004076 1167 0.004622 683 0.005169 388 0.005715 223 0.006261 139 0.006807 86 0.007353 56 0.007899 25 0.008446 16 0.008992 7 0.009538 4 0.01008 4 0.01063 4 0.01118 1 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb PDB file /lmb/home/pemsley/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 50 read successfully DEBUG:: there were 2 types with no dictionary created 46 bond restraints created 82 angle restraints created 2 plane restraints created 8 chiral vol restraints created 138 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A INFO:: glycosidic_linkage type :ALPHA1-4: Link restraints: 1 bond links 3 angle links 0 plane links 0 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 671 non-bonded restraints initial distortion_score: 7133 Initial RMS Z values bonds: 11.36 angles: 3.259 torsions: N/A planes: 0.08353 non-bonded: 0.2373 chiral vol: 0.9035 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 345) at 0.3721 Final Estimated RMS Z Scores: bonds: 0.006172 angles: 0.06489 torsions: N/A planes: 0.0006871 non-bonded: 1.349e-07 chiral vol: 0.03929 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 14.46 debug:: restraints results 1 5 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_multi-carbo-coot-2.pdb_Tue_Dec_27_04:22:07_2016_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. PASS: Mask and difference map Entered testcase - Skeletonize a map PASS: Skeletonize a map Entered testcase - Simple Averaged maps INFO:: map sigmas: normal 0.311081498861313 and diff-map: 0.00107625499367714 PASS: Simple Averaged maps Entered testcase - Make a glycosidic linkage bond-length: 2.97694066606539: bond-length: 1.43915452962871: bond-length-within-tolerance? bond-length 1.43915452962871 with target 1.439 and tolerance 0.04 for atom ((" O4 " "") (1.0 20.0 " O" "") (-3.71707558631897 20.5069255828857 0.834979474544525)) is ((" C1 " "") (1.0 20.0 " C" "") (-3.7664954662323 21.8611373901367 1.31957602500916)) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb PDB file /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 3 links Symmetry available for this molecule INFO:: NCS chain comparison 4/110 Molecule 51 read successfully DEBUG:: there were 1 types with no dictionary INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.047 seconds to read MTZ file INFO:: 0.016 seconds to initialize map INFO:: 0.025 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 1.069e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.027 seconds for contour map INFO:: 0.119 seconds in total reading /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab reading /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/NAG-decorations.tab INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:22:08_2016_modification_0.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:22:08_2016_modification_1.pdb.gz INFO:: link torsion generated from link bond restraint DEBUG tosion quads: 0 [spec: model 1 "B" 464 "" " C2 " ""] [spec: model 1 "B" 464 "" " C1 " ""] [spec: model 1 "B" 141 "" " ND2" ""] [spec: model 1 "B" 141 "" " CG " ""] "Bond-derived synthetic torsion-phi-0" torsion: 128.5 DEBUG tosion quads: 1 [spec: model 1 "B" 141 "" " N " ""] [spec: model 1 "B" 141 "" " CA " ""] [spec: model 1 "B" 141 "" " CB " ""] [spec: model 1 "B" 141 "" " CG " ""] "chi1" torsion: -169.6 DEBUG tosion quads: 2 [spec: model 1 "B" 141 "" " CA " ""] [spec: model 1 "B" 141 "" " CB " ""] [spec: model 1 "B" 141 "" " CG " ""] [spec: model 1 "B" 141 "" " ND2" ""] "chi2" torsion: 179.3 DEBUG tosion quads: 3 [spec: model 1 "B" 464 "" " O5 " ""] [spec: model 1 "B" 464 "" " C5 " ""] [spec: model 1 "B" 464 "" " C6 " ""] [spec: model 1 "B" 464 "" " O6 " ""] "var_3" torsion: -56.09 DEBUG tosion quads: 4 [spec: model 1 "B" 464 "" " C3 " ""] [spec: model 1 "B" 464 "" " C2 " ""] [spec: model 1 "B" 464 "" " N2 " ""] [spec: model 1 "B" 464 "" " C7 " ""] "var_11" torsion: -144.4 ---- contact_info() constructor added link bond contact 8 7 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:22:08_2016_modification_2.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 666 non-bonded restraints initial distortion_score: 1.057e+05 Initial RMS Z values bonds: 0.3607 angles: 0.6064 torsions: N/A planes: 0.6834 non-bonded: 159.9 chiral vol: 0.4449 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 104) at -393.9 Final Estimated RMS Z Scores: bonds: 2.127 angles: 2.149 torsions: N/A planes: 0.5858 non-bonded: 0.09948 chiral vol: 1.625 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 16.06 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:22:08_2016_modification_3.pdb.gz INFO:: replace_coords: 22 atoms updated. INFO:: created 55 restraints created 21 bond restraints created 27 angle restraints created 2 plane restraints created 5 chiral vol restraints Link restraints: 1 bond links 2 angle links 1 plane links 0 trans-peptide links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 2 trans-peptide links 0 parallel plane restraints INFO:: make_restraints(): made 615 non-bonded restraints initial distortion_score: -395.1 Initial RMS Z values bonds: 2.127 angles: 2.149 torsions: N/A planes: 0.5858 non-bonded: 0.1059 chiral vol: 1.625 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -443.9 Final Estimated RMS Z Scores: bonds: 2.123 angles: 2.269 torsions: N/A planes: 0.9219 non-bonded: 0.1087 chiral vol: 1.632 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 16.2 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:22:08_2016_modification_4.pdb.gz INFO:: replace_coords: 22 atoms updated. PASS: Make a glycosidic linkage Entered testcase - Refine an NAG-ASN Link bond-length-within-tolerance? bond-length 1.57996369494848 with target 1.43 and tolerance 0.2 for atom ((" ND2" "") (1.0 16.9300003051758 " N" "") (-15.3005847930908 -0.657990455627441 -7.23382091522217)) is ((" C1 " "") (1.0 45.0 " C" "") (-14.6678981781006 -1.74976575374603 -6.28302145004272)) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 53 read successfully DEBUG:: there were 0 types with no dictionary INFO:: found bad VAL chiral atom: A 1 CB created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.997 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 82) at 0.2477 Final Estimated RMS Z Scores: bonds: 0.01117 angles: 0.09485 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.145 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 16.86 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:22:10_2016_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: undo molecule number set to: 53 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:22:10_2016_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:22:10_2016_modification_0.pdb.gz PDB file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:22:10_2016_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 82) at 0.2477 Final Estimated RMS Z Scores: bonds: 0.01117 angles: 0.09485 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.145 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 16.94 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:22:10_2016_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. PASS: Refine an NAG-ASN Link Entered testcase - Test for flying hydrogens on undo bond-length-within-tolerance? bond-length 0.959977369965271 with target 0.96 and tolerance 0.02 for atom (("HG11" "") (1.0 20.0 " H" "") (3.47049617767334 -0.190978646278381 -1.96916389465332)) is ((" CG1" "") (1.0 20.0 " C" "") (2.87030410766602 -0.207265928387642 -1.22012400627136)) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 54 read successfully DEBUG:: there were 0 types with no dictionary created 17 bond restraints created 31 angle restraints created 0 plane restraints created 1 chiral vol restraints created 49 restraints INFO:: make_restraints(): made 67 non-bonded restraints initial distortion_score: 903.1 Initial RMS Z values bonds: 5.621 angles: 3.433 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.7534 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 184) at 0.4735 Final Estimated RMS Z Scores: bonds: 0.009303 angles: 0.1209 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1378 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 17.7 debug:: restraints results 1 4 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Tue_Dec_27_04:22:11_2016_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. PASS: Test for flying hydrogens on undo Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0 bond-length-within-tolerance? bond-length 0.960000841014185 with target 0.96 and tolerance 0.02 for atom (("HD11" "") (1.0 10.5299997329712 " H" "") (-10.1157665252686 6.52046537399292 7.01385498046875)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1279544830322 5.64627361297607 6.61731767654419)) bond-length-within-tolerance? bond-length 0.959988196371086 with target 0.96 and tolerance 0.02 for atom (("HD12" "") (1.0 10.1300001144409 " H" "") (-9.75977325439453 5.68289756774902 5.73149681091309)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1279544830322 5.64627361297607 6.61731767654419)) bond-length-within-tolerance? bond-length 0.959994915222464 with target 0.96 and tolerance 0.02 for atom (("HD13" "") (1.0 10.5600004196167 " H" "") (-11.0278301239014 5.31346940994263 6.58483028411865)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1279544830322 5.64627361297607 6.61731767654419)) bond-length-within-tolerance? bond-length 0.959987062216489 with target 0.96 and tolerance 0.02 for atom (("HD21" "") (1.0 10.1499996185303 " H" "") (-7.99410676956177 3.15212225914001 7.1437087059021)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55904579162598 3.69594240188599 6.58992290496826)) bond-length-within-tolerance? bond-length 0.959967746929082 with target 0.96 and tolerance 0.02 for atom (("HD22" "") (1.0 10.3000001907349 " H" "") (-9.20832347869873 3.14668321609497 6.14462423324585)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55904579162598 3.69594240188599 6.58992290496826)) bond-length-within-tolerance? bond-length 0.960018167519511 with target 0.96 and tolerance 0.02 for atom (("HD23" "") (1.0 10.6499996185303 " H" "") (-8.02873706817627 4.16671800613403 5.9427924156189)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55904579162598 3.69594240188599 6.58992290496826)) 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: 2044 Initial RMS Z values bonds: 1.152 angles: 0.8476 torsions: N/A planes: 3.056 non-bonded: 81.91 chiral vol: 0.7578 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -1085 Final Estimated RMS Z Scores: bonds: 0.8221 angles: 0.6011 torsions: N/A planes: 0.5901 non-bonded: 0.08438 chiral vol: 0.2084 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 17.79 Refinement elapsed time: 0.02 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:22:11_2016_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. 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: 2.60371930150116: bond-length-within-tolerance? bond-length 2.60371930150116 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.2787017822266 4.48588037490845 19.7545166015625)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.5198211669922 6.67388248443604 19.0824871063232)) 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: 1374 Initial RMS Z values bonds: 14.35 angles: 0.6011 torsions: N/A planes: 0.5901 non-bonded: 0 chiral vol: 0.2084 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 77) at -1184 Final Estimated RMS Z Scores: bonds: 0.2911 angles: 0.2659 torsions: N/A planes: 0.7309 non-bonded: 0 chiral vol: 0.1494 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 17.82 Refinement elapsed time: 0.017 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:22:11_2016_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.51866594553117: bond-length-within-tolerance? bond-length 1.51866594553117 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5558319091797 4.93620586395264 19.4097270965576)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.3152313232422 6.21528291702271 19.1037521362305)) INFO:: wrote mmCIF "coot-test-ala.cif" INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 56 read successfully DEBUG:: there were 1 types with no dictionary 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: 4848 Initial RMS Z values bonds: 0.01199 angles: 0.00654 torsions: N/A planes: 0 non-bonded: 689.9 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 94) at -291.4 Final Estimated RMS Z Scores: bonds: 0.07498 angles: 0.3557 torsions: N/A planes: 0.118 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 18.75 Refinement elapsed time: 0.026 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-ACT.pdb_Tue_Dec_27_04:22:12_2016_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 57 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_modification_2.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_modification_3.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_modification_4.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_modification_6.pdb.gz INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:12_2016_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_Tue_Dec_27_04:22:13_2016_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:13_2016_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:13_2016_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 61 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: /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 50/87 Molecule 62 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 62 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -0.5 is_nucleic_acid_flag 0 console_output 1 --------------------------------------------------- INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID > target seq: DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 163.5 DEBUG:: s.length() 95 DEBUG:: nSelResidues 87 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Tue_Dec_27_04:22:15_2016_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: 269000224 "A" 1 ""] -> ASP [spec: 269000224 "A" 2 ""] -> VAL [spec: 269000224 "A" 3 ""] -> SER [spec: 269000224 "A" 11 ""] -> LEU [spec: 269000224 "A" 12 ""] -> PRO [spec: 269000224 "A" 13 ""] -> PRO [spec: 269000224 "A" 62 ""] -> PRO [spec: 269000224 "A" 63 ""] -> GLY Deletions: [spec: 269000224 "A" 24 ""] [spec: 269000224 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 63 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:16_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 64 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:16_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3hfl.ent PDB file /lmb/home/pemsley/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 65 read successfully DEBUG:: there were 1 types with no dictionary INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.04 seconds to read MTZ file INFO:: 0.009 seconds to initialize map INFO:: 0.02 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 2.004e-11 Map sigma: ....... 0.2604 Map maximum: ..... 1.718 Map minimum: ..... -1.034 INFO:: 0.011 seconds for contour map INFO:: 0.084 seconds in total INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Tue_Dec_27_04:22:17_2016_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.834 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_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_Tue_Dec_27_04:22:17_2016_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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:18_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb PDB file /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 72 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_some-waters-with-ter.pdb_Tue_Dec_27_04:22:18_2016_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: /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb PDB file /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 73 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 -0.03383 stdev: 0.1463) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4 3.2 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 59.89, 3.041, -4.33) is too big to be water INFO:: cluster at xyz = ( 70.01, 19.08, 18.6) is too big to be water INFO:: cluster at xyz = ( 52.98, 9.035, 20.15) is too big to be water INFO:: found 54 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tm+some-waters.pdb_Tue_Dec_27_04:22:19_2016_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 74 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:20_2016_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: /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb PDB file /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 75 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_water-test-no-cell.pdb_Tue_Dec_27_04:22:24_2016_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb PDB file /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pathological-water-test.pdb_Tue_Dec_27_04:22:25_2016_modification_0.pdb.gz INFO:: moved 181 water molecules Symmetry available for this molecule INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.049 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.027 seconds for FFT INFO:: 0.007 seconds for statistics Map mean: ........ 1.069e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.029 seconds for contour map INFO:: 0.113 seconds in total INFO:: Masking around 58 atoms fitting terminal residue with 1000 random trials --- in best_fit_phi_psi() with offset 1 INFO:: Fitting terminal residue without individual rigid body fitting. --- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000 called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:25_2016_modification_0.pdb.gz Symmetry available for this molecule DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 79 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 79 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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:25_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 80 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: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links 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 81 read successfully DEBUG:: there were 1 types with no dictionary INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 82 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 83 read successfully DEBUG:: there were 1 types with no dictionary -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 86 to 85 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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:29_2016_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) 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 ::::: (62 "A" 1 "") #f #f ::::: (62 "A" 4 "") #t #t ::::: (62 "A" 59 "") #t #t ::::: (62 "A" 60 "") #f #f ::::: (62 "A" 61 "") #f #f ::::: (62 "A" 92 "") #t #t ::::: (62 "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 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 bond-length-within-tolerance? bond-length 0.110921496735531 with target 0.0 and tolerance 0.2 for atom ((" C " "") (1.0 15.5799999237061 " C" "") (56.8940010070801 1.29299998283386 19.6700000762939)) is ((" C " "") (1.0 16.7800006866455 " C" "") (56.8856086730957 1.18242847919464 19.6726627349854)) INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 87 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links 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 88 read successfully DEBUG:: there were 0 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: spacegroup: P 21 21 21 INFO:: spacegroup: C 1 2 1 INFO:: Matching/moving molecule number 87 to 88 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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:30_2016_modification_0.pdb.gz INFO:: coordinates transformed by orthogonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 89 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:22:31_2016_modification_0.pdb.gz INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links 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 90 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2goz-manip.pdb PDB file /lmb/home/pemsley/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links Symmetry available for this molecule INFO:: NCS chain comparison 10/85 Molecule 91 read successfully DEBUG:: there were 7 types with no dictionary 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 92 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 93 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 94 read successfully 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. Symmetry available for this molecule Symmetry available for this molecule INFO:: Masking around 32 atoms fitting terminal residue with 1000 random trials --- in best_fit_phi_psi() with offset 1 INFO:: Fitting terminal residue without individual rigid body fitting. --- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000 called fit_terminal_residue_generic() residue-seqnum: 2020 offset: 1 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Tue_Dec_27_04:22:34_2016_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/_lmb_home_pemsley_data_greg-data_insulin.res_Tue_Dec_27_04:22:34_2016_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: 2.4 3.2 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water INFO:: found 28 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Tue_Dec_27_04:22:34_2016_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 99 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 100 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 101 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 102 read successfully INFO:: Creating directory coot-ccp4 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 ((90 "A" 1 "") (90 "A" 2 "") (90 "A" 3 "") (90 "A" 4 "") (90 "A" 5 "") (90 "A" 6 "") (90 "A" 7 "") (90 "A" 8 "") (90 "A" 9 "") (90 "A" 10 "") (90 "A" 11 "") (90 "A" 12 "") (90 "A" 13 "") (90 "A" 14 "") (90 "A" 15 "") (90 "A" 16 "") (90 "A" 17 "") (90 "A" 18 "") (90 "A" 19 "") (90 "A" 20 "") (90 "A" 21 "") (90 "A" 22 "") (90 "A" 23 "") (90 "A" 24 "") (90 "A" 25 "") (90 "A" 26 "") (90 "A" 27 "") (90 "A" 28 "") (90 "A" 29 "") (90 "A" 30 "") (90 "A" 31 "") (90 "A" 32 "") (90 "A" 33 "") (90 "A" 34 "") (90 "A" 35 "") (90 "A" 36 "") (90 "A" 37 "") (90 "A" 38 "") (90 "A" 39 "") (90 "A" 40 "") (90 "A" 41 "") (90 "A" 42 "") (90 "A" 43 "") (90 "A" 44 "") (90 "A" 45 "") (90 "A" 46 "") (90 "A" 47 "") (90 "A" 48 "") (90 "A" 49 "") (90 "A" 50 "") (90 "A" 51 "") (90 "A" 52 "") (90 "A" 53 "") (90 "A" 54 "") (90 "A" 55 "") (90 "A" 56 "") (90 "A" 57 "") (90 "A" 58 "") (90 "A" 59 "") (90 "A" 60 "") (90 "A" 61 "") (90 "A" 62 "") (90 "A" 63 "") (90 "A" 64 "") (90 "A" 65 "") (90 "A" 66 "") (90 "A" 67 "") (90 "A" 68 "") (90 "A" 69 "") (90 "A" 70 "") (90 "A" 71 "") (90 "A" 72 "") (90 "A" 73 "") (90 "A" 74 "") (90 "A" 75 "") (90 "A" 76 "") (90 "A" 77 "") (90 "A" 78 "") (90 "A" 79 "") (90 "A" 80 "") (90 "A" 81 "") (90 "A" 82 "") (90 "A" 83 "") (90 "A" 84 "") (90 "A" 85 "") (90 "A" 86 "") (90 "A" 87 "") (90 "A" 88 "") (90 "A" 89 "") (90 "A" 90 "") (90 "A" 91 "") (90 "A" 92 "") (90 "A" 93 "") (90 "B" 1 "") (90 "B" 2 "") (90 "B" 3 "") (90 "B" 4 "") (90 "B" 5 "") (90 "B" 6 "") (90 "B" 7 "") (90 "B" 8 "") (90 "B" 9 "") (90 "B" 10 "") (90 "B" 11 "") (90 "B" 12 "") (90 "B" 13 "") (90 "B" 14 "") (90 "B" 15 "") (90 "B" 16 "") (90 "B" 17 "") (90 "B" 18 "") (90 "B" 19 "") (90 "B" 20 "") (90 "B" 21 "") (90 "B" 22 "") (90 "B" 23 "") (90 "B" 24 "") (90 "B" 25 "") (90 "B" 26 "") (90 "B" 27 "") (90 "B" 28 "") (90 "B" 29 "") (90 "B" 30 "") (90 "B" 31 "") (90 "B" 32 "") (90 "B" 33 "") (90 "B" 34 "") (90 "B" 35 "") (90 "B" 36 "") (90 "B" 37 "") (90 "B" 38 "") (90 "B" 39 "") (90 "B" 40 "") (90 "B" 41 "") (90 "B" 42 "") (90 "B" 43 "") (90 "B" 44 "") (90 "B" 45 "") (90 "B" 46 "") (90 "B" 47 "") (90 "B" 48 "") (90 "B" 49 "") (90 "B" 50 "") (90 "B" 51 "") (90 "B" 52 "") (90 "B" 53 "") (90 "B" 54 "") (90 "B" 55 "") (90 "B" 56 "") (90 "B" 57 "") (90 "B" 58 "") (90 "B" 59 "") (90 "B" 60 "") (90 "B" 61 "") (90 "B" 62 "") (90 "B" 63 "") (90 "B" 64 "") (90 "B" 65 "") (90 "B" 66 "") (90 "B" 67 "") (90 "B" 68 "") (90 "B" 69 "") (90 "B" 70 "") (90 "B" 71 "") (90 "B" 72 "") (90 "B" 73 "") (90 "B" 74 "") (90 "B" 75 "") (90 "B" 76 "") (90 "B" 77 "") (90 "B" 78 "") (90 "B" 79 "") (90 "B" 80 "") (90 "B" 81 "") (90 "B" 82 "") (90 "B" 83 "") (90 "B" 84 "") (90 "B" 85 "") (90 "B" 86 "") (90 "B" 87 "") (90 "B" 88 "") (90 "B" 89 "") (90 "B" 90 "") (90 "B" 91 "") (90 "B" 92 "") (90 "B" 93 "") (90 "B" 94 "") (90 "B" 95 "") (90 "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 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 : 11617 : with complete description : 11617 : 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 6.5.019: Refmac_5.8.0135 version 5.8.0135 : 01/10/15##
: ###############################################################
: User: unknown  Run date: 27/12/2016 Run time: 04:22:37 
:
:
: 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
:===> 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 : /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/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          : 11617
:                with complete description    : 11617
:  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: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/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 =         0.75
:             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  0.351INFO:: 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 103 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:22:44_2016_modification_0.pdb.gz
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:22:44_2016_modification_1.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 104 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: /lmb/home/pemsley/data/greg-data/test-LIG.pdb
 PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 105 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: /lmb/home/pemsley/data/greg-data/test-LIG.pdb
 PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 106 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:22:44_2016_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: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 107 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: /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
 PDB file /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
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 113 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.258 seconds to read MTZ file
INFO:: 0.153 seconds to initialize map
INFO:: 0.125 seconds for FFT
INFO:: 0.024 seconds for statistics
      Map mean: ........ -8.79e-07
      Map sigma: ....... 0.1712
      Map maximum: ..... 1.343
      Map minimum: ..... -0.6954
INFO:: 0.01 seconds for contour map
INFO:: 0.57 seconds in total
INFO:: making difference map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.151 seconds to read MTZ file
INFO:: 0.003 seconds to initialize map
INFO:: 0.122 seconds for FFT
INFO:: 0.024 seconds for statistics
      Map mean: ........ 2.094e-06
      Map sigma: ....... 0.03339
      Map maximum: ..... 0.3661
      Map minimum: ..... -0.1917
INFO:: 0.005 seconds for contour map
INFO:: 0.305 seconds in total
INFO:: ligand number 0 is molecule number 107   with wiggly flag: 0
ligand_search_install_wiggly_ligands: returning wlig 0x12f82050
Executing ligand search internal using wlig_p 0x12f82050
in execute_ligand_search_internal() import maps from mol 114
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
debug:: n_ligands_for_cluster() top_score 4.042 and 4 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 2.007 and 9 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 2.092 and 4 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 1.857 and 6 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 1.387 and 10 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 1.611 and 8 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 2.1 and 8 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 1.691 and 7 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 2.123 and 2 are decent out of 12
Symmetry available for this molecule
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 
debug:: n_ligands_for_cluster() top_score 1.841 and 6 are decent out of 12
Symmetry available for this molecule
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: 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 127 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_Tue_Dec_27_04:23:03_2016_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:23:03_2016_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:23:03_2016_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:23:03_2016_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/dipole-residues.pdb
 PDB file /lmb/home/pemsley/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 129 read successfully
DEBUG:: there were 0 types with no dictionary 
WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
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 130 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 130
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 130
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb
 PDB file /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 131 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.049 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.026 seconds for FFT
INFO:: 0.004 seconds for statistics
      Map mean: ........ 1.069e-09
      Map sigma: ....... 0.3115
      Map maximum: ..... 2.978
      Map minimum: ..... -0.875
INFO:: 0.023 seconds for contour map
INFO:: 0.103 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 131

Sequence: ?EYTVITPGARTR
Confidence: 1

From    : HEYTVITPGARTR
Chain id: 0	Offset: 53
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Tue_Dec_27_04:23:08_2016_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_Tue_Dec_27_04:23:09_2016_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 135 to 135
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_Tue_Dec_27_04:23:10_2016_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal 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: /lmb/home/pemsley/data/greg-data/1wly.pdb
 PDB file /lmb/home/pemsley/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 136 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1yb5.pdb
 PDB file /lmb/home/pemsley/data/greg-data/1yb5.pdb has been read.
Spacegroup: P 21 21 2
INFO:: Found 1 models
   Model 1 had 0 links
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 137 read successfully
DEBUG:: there were 2 types with no dictionary 
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: reference 136 has 750 atoms selected
INFO:: moving    137 has 842 atoms selected
superposing...
number of Ca atoms in selections: 110 (moving) and 100 (reference)
Another Go...

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

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

 Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY
 Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI

INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_1yb5.pdb_Tue_Dec_27_04:23:11_2016_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|   -0.9117,   -0.3803,    0.1557|
|   -0.3625,    0.9227,     0.131|
|   -0.1935,   0.06299,   -0.9791|
(     70.65,     7.793,     21.29)
  Rotation - polar (omega,phi,kappa)  87.1413 101.0220 169.7385
  Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277
  Translation - Angstroms             70.6538 7.7930 21.2852 
INFO: core rmsd achieved: 1.0199 Angstroems
      number of residues in reference structure: 322
      number of residues in moving structure:    324
      number of residues in aligned sections (reference):  100
      number of residues in aligned sections (moving):     110
      number of aligned residues:  95
      number of gaps:              4
      number of misdirections:     0
      number of SSE combinations:  4.0000
      sequence identity:           30.5263%
WARNING:: Error reading /lmb/home/pemsley/data/greg-data/1pyd.pdb
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2qd9.pdb
 PDB file /lmb/home/pemsley/data/greg-data/2qd9.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 138 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2gtn.pdb
 PDB file /lmb/home/pemsley/data/greg-data/2gtn.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 0/337
Molecule 139 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: reference 138 has 169 atoms selected
INFO:: moving    139 has 169 atoms selected
superposing...
number of Ca atoms in selections: 21 (moving) and 21 (reference)
Another Go...

     Moving      Reference   Distance(/A)
      A 140  <--->  A 140  :  0.1804
      A 141  <--->  A 141  :  0.0760
      A 142  <--->  A 142  :  0.1052
      A 143  <--->  A 143  :  0.1246
      A 144  <--->  A 144  :  0.1370
      A 145  <--->  A 145  :  0.1380
      A 146  <--->  A 146  :  0.1662
      A 147  <--->  A 147  :  0.2744
      A 148  <--->  A 148  :  0.2728
      A 149  <--->  A 149  :  0.1173
      A 150  <--->  A 150  :  0.1684
      A 151  <--->  A 151  :  0.0928
      A 152  <--->  A 152  :  0.1200
      A 153  <--->  A 153  :  0.1281
      A 154  <--->  A 154  :  0.2539
      A 155  <--->  A 155  :  0.6351
      A 156  <--->  A 156  :  0.1300
      A 157  <--->  A 157  :  0.1478
      A 158  <--->  A 158  :  0.2238
      A 159  <--->  A 159  :  0.2271
      A 160  <--->  A 160  :  0.2372

 Moving: YIHSADIIHRDLKPSNLAVNE
 Target: YIHSADIIHRDLKPSNLAVNE

INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2gtn.pdb_Tue_Dec_27_04:23:13_2016_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|    0.9998,  0.009845,  -0.01938|
| -0.009814,         1,  0.001689|
|    0.0194, -0.001498,    0.9998|
(    0.3207,    0.6598,    0.8819)
  Rotation - polar (omega,phi,kappa)  116.8035 -94.6984 1.2491
  Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832
  Translation - Angstroms             0.3207 0.6598 0.8819 
INFO: core rmsd achieved: 0.2210 Angstroems
      number of residues in reference structure: 330
      number of residues in moving structure:    337
      number of residues in aligned sections (reference):  21
      number of residues in aligned sections (moving):     21
      number of aligned residues:  21
      number of gaps:              0
      number of misdirections:     0
      number of SSE combinations:  1.0000
      sequence identity:           100.0000%
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 140 read successfully
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.0500 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0270 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:: 0.0240 seconds for contour map
INFO:: 0.1050 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:: 409600 out of 409600 (100.0000%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: 0.0006 st.d: 0.3256
Map statistics: min: -1.4696, max: 2.2923
   -1.4225    2
   -1.3285    5
   -1.2344    5
   -1.1404    10
   -1.0463    9
   -0.9523    37
   -0.8583    141
   -0.7642    493
   -0.6702    1554
   -0.5761    4667
   -0.4821    12350
   -0.3880    26465
   -0.2940    43650
   -0.1999    55555
   -0.1059    57553
   -0.0118    50690
    0.0822    40145
    0.1763    30074
    0.2703    23268
    0.3644    17859
    0.4584    13062
    0.5524    9524
    0.6465    7028
    0.7405    4917
    0.8346    3611
    0.9286    2439
    1.0227    1610
    1.1167    1087
    1.2108    736
    1.3048    442
    1.3989    252
    1.4929    160
    1.5870    83
    1.6810    49
    1.7751    24
    1.8691    17
    1.9631    13
    2.0572    4
    2.1512    5
    2.2453    4
    2.3393    1
INFO:: installing ghost map with name :Map 141 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: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
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 146 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:23:16_2016_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:23:16_2016_modification_1.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:23:16_2016_modification_2.pdb.gz
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: 146 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 146 and ichain: 0
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 0
   Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 90/93
First atom of 720 in first  selection 1/A/1 {ASP}/ N   altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 724 in second selection 1/B/4 {GLY}/ N   altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100
INFO:: LSQ matched 90 atoms
INFO:: 90 matched atoms had: 
   mean devi: 0.3643
    rms devi: 0.4571
    max devi: 2.1351
    min devi: 0.0881
   find_ncs_matrix returns (LSQ) 
|    0.9705,  -0.04634,   -0.2366|
|    0.2357,    0.3884,    0.8908|
|   0.05061,   -0.9203,    0.3878|
(      37.8,    -17.18,     13.82)
   Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
   Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:23:16_2016_modification_3.pdb.gz
INFO:: mutate 2 A to a TRP
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:23:16_2016_modification_4.pdb.gz
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 146 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 146 and ichain: 0
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 0
   Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 92/93
First atom of 727 in first  selection 1/A/1 {ASP}/ N   altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 745 in second selection 1/B/1 {ASP}/ N   altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700
INFO:: LSQ matched 93 atoms
INFO:: 93 matched atoms had: 
   mean devi: 0.3427
    rms devi: 0.4454
    max devi: 2.1352
    min devi: 0.0124
   find_ncs_matrix returns (LSQ) 
|    0.9705,  -0.04643,   -0.2365|
|    0.2356,    0.3891,    0.8906|
|   0.05068,     -0.92,    0.3886|
(      37.8,    -17.17,     13.81)
   Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
   Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:23:16_2016_modification_5.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1t6q.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1t6q.ent has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
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 147 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: mutate 50 A to a ASP
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Dec_27_04:23:17_2016_modification_0.pdb.gz
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: 147 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 147 and ichain: 0
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 0
   Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first  selection 1/A/7 {GLY}/ N   altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 893 in second selection 1/B/6 {CYS}/ N   altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had: 
   mean devi: 0.2048
    rms devi: 0.2651
    max devi: 1.1707
    min devi: 0.0160
   find_ncs_matrix returns (LSQ) 
|    0.5407,    0.4775,    0.6926|
|   -0.4862,   -0.4944,    0.7205|
|    0.6865,   -0.7263,  -0.03511|
(    -28.15,     65.89,      42.9)
   Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first  selection 1/A/7 {GLY}/ N   altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 881 in second selection 1/C/7 {GLY}/ N   altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had: 
   mean devi: 0.2275
    rms devi: 0.3035
    max devi: 1.6549
    min devi: 0.0661
   find_ncs_matrix returns (LSQ) 
|    0.5303,   -0.4851,    0.6953|
|    0.4758,   -0.5085,   -0.7177|
|    0.7017,    0.7114,  -0.03884|
(     18.19,     77.78,    -25.69)
   Adding ghost with name: NCS found from matching Chain C onto Chain A
INFO:: set_ncs_master_chain Constructed 2 ghosts
   Ghost info:: NCS found from matching Chain B onto Chain A
   Ghost info:: NCS found from matching Chain C onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Dec_27_04:23:17_2016_modification_1.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Dec_27_04:23:17_2016_modification_2.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
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 148 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 148 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 149 to 148
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had: 
   mean devi: 0.2239
    rms devi: 0.2350
    max devi: 0.3369
    min devi: 0.0588
INFO:: Axis orientation: (    0.7368,    0.6481,    0.1925)
INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Dec_27_04:23:20_2016_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|    0.3395,    0.5177,    0.7853|
|    0.8624,     0.162,   -0.4796|
|   -0.3755,    0.8401,   -0.3915|
(     90.55,    -91.12,    -47.52)
INFO:: fractional coordinates matrix:
|    0.8374,    0.1106,    0.6656|
|    0.9958,   -0.3359,   -0.7249|
|   -0.2868,    0.6992,   -0.3915|
(    0.4296,    -1.191,    -0.411)
Symmetry available for this molecule
INFO:: Matching/moving molecule number 150 to 148
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__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Dec_27_04:23:20_2016_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal 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 151 to 148
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__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Dec_27_04:23:20_2016_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal 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: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
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 152 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz
Number of OBSERVED reflections: 20903
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 112, 112, 150)
INFO:: 0.0660 seconds to read MTZ file
INFO:: 0.0340 seconds to initialize map
INFO:: 0.0460 seconds for FFT
INFO:: 0.0060 seconds for statistics
      Map mean: ........ -0.0000
      Map sigma: ....... 0.2241
      Map maximum: ..... 1.7219
      Map minimum: ..... -0.8818
INFO:: 0.0120 seconds for contour map
INFO:: 0.1640 seconds in total
INFO:: NCS chain comparison 62/67
First atom of 540 in first  selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 506 in second selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.4989
    rms devi: 2.7962
    max devi: 6.6860
    min devi: 0.4401
   find_ncs_matrix returns (LSQ) 
|    0.7026,    0.6024,   -0.3788|
|    0.1278,    0.4169,    0.8999|
|       0.7,   -0.6807,    0.2159|
(     5.528,     36.75,    -101.2)
INFO:: NCS chain comparison 66/67
First atom of 540 in first  selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 535 in second selection 1/C/190 {GLN}/ N   altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 66 atoms
INFO:: 66 matched atoms had: 
   mean devi: 1.9713
    rms devi: 2.1729
    max devi: 4.5411
    min devi: 0.4295
   find_ncs_matrix returns (LSQ) 
|   -0.4445,   -0.8903,  -0.09887|
|    -0.893,    0.4317,    0.1271|
|  -0.07049,    0.1448,   -0.9869|
(    -8.624,     7.402,    -127.7)
INFO:: NCS chain comparison 61/67
First atom of 540 in first  selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 497 in second selection 1/D/193 {SER}/ N   altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had: 
   mean devi: 3.7042
    rms devi: 4.0859
    max devi: 9.4383
    min devi: 0.2858
   find_ncs_matrix returns (LSQ) 
|   -0.7198,   -0.6079,    0.3353|
|   -0.5986,    0.2989,   -0.7432|
|    0.3516,   -0.7356,    -0.579|
(     36.14,     -61.4,    -149.3)
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain D onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
|    0.7026,    0.6024,   -0.3788|
|    0.1278,    0.4169,    0.8999|
|       0.7,   -0.6807,    0.2159|
(     5.528,     36.75,    -101.2)
inverse of reference matcher transformation:
|    0.7026,    0.1278,       0.7|
|    0.6024,    0.4169,   -0.6807|
|   -0.3788,    0.8999,    0.2159|
(     62.25,    -87.53,    -9.128)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
Reference matcher: 0 and 1
|   -0.4445,   -0.8903,  -0.09887|
|    -0.893,    0.4317,    0.1271|
|  -0.07049,    0.1448,   -0.9869|
(    -8.624,     7.402,    -127.7)
inverse of reference matcher transformation:
|   -0.4445,    -0.893,  -0.07049|
|   -0.8903,    0.4317,    0.1448|
|  -0.09887,    0.1271,   -0.9869|
(    -6.223,     7.613,    -127.8)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
Reference matcher: 0 and 2
|   -0.7198,   -0.6079,    0.3353|
|   -0.5986,    0.2989,   -0.7432|
|    0.3516,   -0.7356,    -0.579|
(     36.14,     -61.4,    -149.3)
inverse of reference matcher transformation:
|   -0.7198,   -0.5986,    0.3516|
|   -0.6079,    0.2989,   -0.7356|
|    0.3353,   -0.7432,    -0.579|
(     41.75,    -69.53,    -144.2)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
INFO:: There were 4.0000 maps contributing to the average
INFO:: rescaling by 0.2500
INFO:: 313712 out of 313712 (100.0000%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
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 153 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain D onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
|    0.7026,    0.6024,   -0.3788|
|    0.1278,    0.4169,    0.8999|
|       0.7,   -0.6807,    0.2159|
(     5.528,     36.75,    -101.2)
inverse of reference matcher transformation:
|    0.7026,    0.1278,       0.7|
|    0.6024,    0.4169,   -0.6807|
|   -0.3788,    0.8999,    0.2159|
(     62.25,    -87.53,    -9.128)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
Reference matcher: 0 and 1
|   -0.4445,   -0.8903,  -0.09887|
|    -0.893,    0.4317,    0.1271|
|  -0.07049,    0.1448,   -0.9869|
(    -8.624,     7.402,    -127.7)
inverse of reference matcher transformation:
|   -0.4445,    -0.893,  -0.07049|
|   -0.8903,    0.4317,    0.1448|
|  -0.09887,    0.1271,   -0.9869|
(    -6.223,     7.613,    -127.8)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
Reference matcher: 0 and 2
|   -0.7198,   -0.6079,    0.3353|
|   -0.5986,    0.2989,   -0.7432|
|    0.3516,   -0.7356,    -0.579|
(     36.14,     -61.4,    -149.3)
inverse of reference matcher transformation:
|   -0.7198,   -0.5986,    0.3516|
|   -0.6079,    0.2989,   -0.7356|
|    0.3353,   -0.7432,    -0.579|
(     41.75,    -69.53,    -144.2)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
INFO:: There were 4.0000 maps contributing to the average
INFO:: rescaling by 0.2500
INFO:: 313712 out of 313712 (100.0000%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
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 153 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain D onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
|    0.7026,    0.6024,   -0.3788|
|    0.1278,    0.4169,    0.8999|
|       0.7,   -0.6807,    0.2159|
(     5.528,     36.75,    -101.2)
inverse of reference matcher transformation:
|    0.7026,    0.1278,       0.7|
|    0.6024,    0.4169,   -0.6807|
|   -0.3788,    0.8999,    0.2159|
(     62.25,    -87.53,    -9.128)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
Reference matcher: 0 and 1
|   -0.4445,   -0.8903,  -0.09887|
|    -0.893,    0.4317,    0.1271|
|  -0.07049,    0.1448,   -0.9869|
(    -8.624,     7.402,    -127.7)
inverse of reference matcher transformation:
|   -0.4445,    -0.893,  -0.07049|
|   -0.8903,    0.4317,    0.1448|
|  -0.09887,    0.1271,   -0.9869|
(    -6.223,     7.613,    -127.8)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
Reference matcher: 0 and 2
|   -0.7198,   -0.6079,    0.3353|
|   -0.5986,    0.2989,   -0.7432|
|    0.3516,   -0.7356,    -0.579|
(     36.14,     -61.4,    -149.3)
inverse of reference matcher transformation:
|   -0.7198,   -0.5986,    0.3516|
|   -0.6079,    0.2989,   -0.7356|
|    0.3353,   -0.7432,    -0.579|
(     41.75,    -69.53,    -144.2)
boxing over uvw = (   -0.7364,   -0.9448,    -0.679) to uvw = (    0.7947,   0.04686,   -0.4302)
INFO:: There were 4.0000 maps contributing to the average
INFO:: rescaling by 0.2500
INFO:: 313712 out of 313712 (100.0000%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
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: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 162 read successfully
DEBUG:: there were 0 types with no dictionary 
Entering test: OXT in restraints?
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/
There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif
There are 2 data in /lmb/home/pemsley/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: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/
There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/hideous-OXT.pdb
 PDB file /lmb/home/pemsley/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 13 non-bonded restraints
initial distortion_score: 1241.5407
    Initial RMS Z values
bonds:      3.7208
angles:     7.4688
torsions:   0.2764
planes:     16.9011
non-bonded: 0.0000
chiral vol: 1.2266
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 398) at 0.0088
    Final Estimated RMS Z Scores:
bonds:      0.0009
angles:     0.0235
torsions:   0.0400
planes:     0.0009
non-bonded: 0.0000
chiral vol: 0.0024
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
refinement_took 0.0120 seconds
OXT out of plane distance: 0.0000
OXT->O distance: 2.1104
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: /lmb/home/pemsley/data/greg-data/frag-2wot.pdb
 PDB file /lmb/home/pemsley/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
bad residues for phi,psi calculation
bad residues for phi,psi calculation
PASS: Residues for phi,psi are close enough to be considered linked
   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.       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_5.8.0135:  End of Refmac_5.8.0135  
:Times: User:       6.2s System:    0.1s Elapsed:     0:07  
:
: : 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 Entered testcase - Pyrogen Runs OK? PASS: Pyrogen Runs OK? 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 131 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 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 2 "/lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb" 3 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 4 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 5 "/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 6 "test-3hfl.map" 7 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 8 "mainchain" 9 "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 10 "atom selection from tutorial-add-terminal-1-test.pdb" 11 "/lmb/home/pemsley/data/greg-data/frag-2wot.pdb" 12 "sphere selection from tutorial-modern.pdb" 14 "/lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb" 15 "/lmb/home/pemsley/data/greg-data/res098.pdb" 16 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 17 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 18 "/lmb/home/pemsley/data/greg-data/pdb3knw.ent" 19 "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 22 "/lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb" 23 "/lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 24 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 25 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 26 "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 27 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 28 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 29 "/lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb" 30 "/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb" 31 "Copy_of_/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb" 32 "/lmb/home/pemsley/data/greg-data/coords-B3A.pdb" 33 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 34 "/lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb" 35 "/lmb/home/pemsley/data/greg-data/val.pdb" 36 "/lmb/home/pemsley/data/greg-data/2yie-frag.pdb" 37 "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 38 "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 39 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 40 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 41 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 42 "Generic Masked Map" 43 "difference-map" 46 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 47 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 48 "averaged-map" 49 "difference-map" 50 "/lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb" 51 "/lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb" 52 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 53 "/lmb/home/pemsley/data/greg-data/monomer-VAL.pdb" 54 "/lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 55 "atom selection from tutorial-modern.pdb" 56 "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 57 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 58 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 59 "atom selection from tutorial-modern.pdb" 60 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 61 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 62 "/lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb" 63 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 64 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 65 "/lmb/home/pemsley/data/greg-data/pdb3hfl.ent" 66 "/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 67 "Ideal-A-form-RNA" 68 "Ideal-A-form-RNA" 69 "Ideal-A-form-DNA" 70 "Ideal-A-form-DNA" 71 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 72 "/lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb" 73 "/lmb/home/pemsley/data/greg-data/tm+some-waters.pdb" 74 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 75 "/lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb" 76 "/lmb/home/pemsley/data/greg-data/pathological-water-test.pdb" 77 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 78 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 79 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 80 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 81 "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 82 "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 83 "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 84 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_81" 85 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 86 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 87 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 88 "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 89 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 90 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 91 "/lmb/home/pemsley/data/greg-data/2goz-manip.pdb" 92 "/lmb/home/pemsley/data/greg-data/HOF.RES" 93 "/lmb/home/pemsley/data/greg-data/hollander.ins" 96 "/lmb/home/pemsley/data/greg-data/insulin.fcf Diff-SigmaA" 97 "atom selection from insulin.res" 98 "atom selection from insulin.res" 100 "/lmb/home/pemsley/data/greg-data/horma-p21.res" 101 "new-horma.ins" 102 "/lmb/home/pemsley/data/greg-data/crash.hat" 103 "coot-ccp4/monomer-3GP.pdb" 104 "/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb" 105 "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 106 "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 107 "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 108 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 109 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 110 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 111 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 112 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 113 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 114 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 115 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 116 "Masked (by protein)" 117 "Fitted ligand #0-0" 118 "Fitted ligand #1-0" 119 "Fitted ligand #2-0" 120 "Fitted ligand #3-0" 121 "Fitted ligand #4-0" 122 "Fitted ligand #5-0" 123 "Fitted ligand #6-0" 124 "Fitted ligand #7-0" 125 "Fitted ligand #8-0" 126 "Fitted ligand #9-0" 127 "coot-ccp4/monomer-3GP.pdb" 128 "Copy_of_coot-ccp4/monomer-3GP.pdb" 129 "/lmb/home/pemsley/data/greg-data/dipole-residues.pdb" 130 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 131 "/lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb" 132 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 133 "Ideal-A-form-RNA" 136 "/lmb/home/pemsley/data/greg-data/1wly.pdb" 137 "/lmb/home/pemsley/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 153 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 153 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 153 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 120 # of expected passes 120 # 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 120 # of expected passes 120 # 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 ObjectCache: Leaked 0003 refs to ObjectCache: Leaked 0003 refs to test_coot: coot test passed