testing with greg testing with greg currently we are here: /home/paule/autobuild/building/emsley-vm-ubuntu1404_2015-09-06__T10_36_03/coot-0.8.3-pre Sun Sep 6 11:51:01 BST 2015 WARNING:: ccp4 setup file setup-ccp4 does not exist. /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif INFO:: Reading coordinate file: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Importing python module coot using command from coot import * INFO:: coot.py imported Running python script /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Loading: redefine_functions.py Loading: coot_utils.py Loading: filter.py Loading: coot_lsq.py Loading: shelx.py Loading: get_ebi.py INFO:: Creating directory coot-download Loading: local_code.py Loading: hello.py Good Morning None, Welcome to Coot. 0.8.3-pre (set-display-intro-string "Good Morning None, Welcome to Coot. 0.8.3-pre") Loading: mutate.py Loading: refmac.py Loading: libcheck.py Loading: gap.py Loading: fitting.py Loading: raster3d.py Loading: povray.py Loading: remote_control.py Loading: generic_objects.py Loading: ncs.py Loading: parse_pisa_xml.py Loading: cns2coot.py Loading: clear_backup.py Loading: tips.py Loading: prodrg_import.py Loading: dictionary_generators.py Loading: jligand.py Loading: americanisms.py Loading: group_settings.py Loading: brute_lsqman.py INFO:: preferences directory /home/paule/.coot-preferences does not exist. Won't read preferences. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/scheme (set-display-intro-string "Good morning root. Welcome to Coot") (set-display-lists-for-maps 0) INFO:: preferences directory /home/paule/.coot-preferences does not exist. Won't read preferences. (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: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary Molecule number -5 is not a valid model molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/2WF6.cif mmCIF file /home/paule/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 1 read successfully DEBUG:: there were 3 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "ALF" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALF.cif INFO:: using standard CCP4 Refmac dictionary to search for "MG" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MG.cif INFO:: using standard CCP4 Refmac dictionary to search for "BG6" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/b/BG6.cif in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Reading coordinate file: /home/paule/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/paule/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 2 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Creating directory coot-backup INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Sun_Sep__6_11:51:20_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Sun_Sep__6_11:51:20_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Sun_Sep__6_11:51:20_2015_modification_2.pdb.gz WARNING:: Error reading bogus.map Read map bogus.map failed WARNING:: Can't find file bogus.mtz INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.042 seconds to read MTZ file INFO:: 0.012 seconds to initialize map INFO:: 0.055 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.031 seconds for contour map INFO:: 0.143 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.032 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.018 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.05439e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.018 seconds for contour map INFO:: 0.07 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.041 seconds to read MTZ file INFO:: 0.01 seconds to initialize map INFO:: 0.021 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 8.66951e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.006 seconds for contour map INFO:: 0.082 seconds in total INFO:: map file type was determined to be CCP4 type attempting to read CCP4 map: test-3hfl.map closing CCP4 map: test-3hfl.map Map statistics: mean: 8.66951e-11 st.d: 0.260405 Map statistics: min: -1.03389, max: 1.71787 -0.999495 1 -0.930701 8 -0.861907 23 -0.793113 96 -0.724319 305 -0.655525 714 -0.586731 1587 -0.517937 2927 -0.449143 5202 -0.380349 7937 -0.311555 11655 -0.242761 16895 -0.173967 24542 -0.105173 34962 -0.0363794 43098 0.0324146 41219 0.101209 29087 0.170003 15906 0.238797 8720 0.307591 6095 0.376384 4870 0.445178 4308 0.513972 3717 0.582766 3304 0.65156 2688 0.720354 2065 0.789148 1620 0.857942 1097 0.926736 786 0.99553 479 1.06432 257 1.13312 146 1.20191 73 1.27071 35 1.3395 20 1.40829 14 1.47709 11 1.54588 7 1.61468 3 1.68347 0 1.75226 1 INFO:: n grid points: 276480 INFO:: mean before filtering: 8.66951e-11 INFO:: variance before filtering: 0.0678109 INFO:: filter by ignoring 210 of 276480 counts ( = 0.07595%) with values around -0.005422 from bin 3737 of 10000 Map mean: ........ 4.066e-06 Map rmsd: ........ 0.2604 Map maximum: ..... 1.718 Map minimum: ..... -1.034 WARNING:: Error reading . . is a directory. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 7 read successfully DEBUG:: there were 0 types with no dictionary /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures successfully opened Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb 108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb 9 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb 142 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb 208 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb 123 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb 136 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb 171 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb 108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb 364 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb 51 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb 174 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb 155 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb 349 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb 14 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb 64 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb 106 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb 131 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb 33 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb 129 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb 137 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb 143 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb 247 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb There was an error reading /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. ERROR 42 READ: Duplicate sequence number and insertion code. LINE #868 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb 520 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb 52 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb 205 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb 75 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb 23 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb 228 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb 318 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb 20 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb 149 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb 326 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb 68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb 13 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb 29 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb 72 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb 226 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb 4 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb 24 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb 543 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb 45 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb 494 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb 54 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb 0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb 140 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb 127 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb 68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb 294 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb 119 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb 35 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb 218 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb 411 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb 145 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb 172 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb 56 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb INFO:: 8375 fragments found in total of which 0 were 5 peptides target fragment start res: 10 had 29 db fragment hits, ilength=6 target fragment start res: 13 had 1772 db fragment hits, ilength=6 breaking out of match_target_fragment 6 with iresno= 16 merge fragments 10 to 20 with 2 fit sets to merge The merging is complete mainchain_fragment from 10 to 20 done mainchain_fragment successfully set cell and symmetry Symmetry available for this molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 9 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 41 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 0 ALA N :: xyz = ( 49.42, 12.37, 4.385) A 0 ALA C :: xyz = ( 50.92, 13, 2.535) A 0 ALA CA :: xyz = ( 50.36, 13.37, 3.907) A 0 ALA O :: xyz = ( 52.12, 13.03, 2.265) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_11:51:24_2015_modification_0.pdb.gz Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_11:51:24_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 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_Sun_Sep__6_11:51:24_2015_modification_0.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_11:51:24_2015_modification_1.pdb.gz INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_11:51:24_2015_modification_2.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/rotamer-test-fragment.pdb PDB file /home/paule/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 14 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading rotamer probability tables... primitive chis: Failure to find correct atom quads in residue atoms quad needed: : N : : CA : : CB : : OG1: INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""] INFO:: Reading coordinate file: /home/paule/data/greg-data/res098.pdb PDB file /home/paule/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 15 read successfully DEBUG:: there were 0 types with no dictionary created 6 bond restraints created 6 angle restraints created 0 plane restraints created 1 chiral vol restraints created 13 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 9 non-bonded restraints initial distortion_score: 36.32 Initial RMS Z values bonds: 0.4049 angles: 0.4529 torsions: N/A planes: 2.851 non-bonded: 0 chiral vol: 0.1627 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 198) at 10.68 Final Estimated RMS Z Scores: bonds: 0.08647 angles: 0.7939 torsions: N/A planes: 0.8033 non-bonded: 0 chiral vol: 0.6906 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 5.505 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Sun_Sep__6_11:51:26_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 16 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.031 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.023 seconds for contour map INFO:: 0.074 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:26_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:26_2015_modification_1.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 11.75 INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3knw.ent PDB file /home/paule/data/greg-data/pdb3knw.ent has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 30 links Symmetry available for this molecule INFO:: NCS chain comparison 185/199 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 18 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "EDO" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3knw.ent_Sun_Sep__6_11:51:26_2015_modification_0.pdb.gz load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "redefine-functions.scm" load "json-reader.scm" load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" load "local-code.scm" load "hello.scm" Good morning root. Welcome to Coot 0.8.3-pre. load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "parse-pisa-xml.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "prodrg-import.scm" load "dictionary-generators.scm" load "jligand.scm" load "americanisms.scm" load "group-settings.scm" === greg-tests tests === Loading greg-tests/begin.grg ... =============================================================== ==================== Testing ================================== =============================================================== Loaded greg-tests/begin.grg Running 01-pdb+mtz.scm ... Entered testcase - Post Go To Atom no molecules PASS: Post Go To Atom no molecules Entered testcase - Close bad molecule PASS: Close bad molecule Entered testcase - Read coordinates test PASS: Read coordinates test Entered testcase - New molecule from bogus molecule PASS: New molecule from bogus molecule Entered testcase - Don't crash on empty NCS from mmCIF file closing molecule number 1 PASS: Don't crash on empty NCS from mmCIF file Entered testcase - New molecule from bogus atom selection INFO:: pre-n-molecules 2 post-n-molecules 2 PASS: New molecule from bogus atom selection Entered testcase - ins code change and Goto atom over an ins code break pre and post ins codes: "" "A" pass: ("A" 68 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "A" " CA ") pass: ("A" 68 "" " CA ") pass: ("A" 66 "" " CA ") PASS: ins code change and Goto atom over an ins code break Entered testcase - Read a bogus map PASS: Read a bogus map Entered testcase - Read MTZ test PASS: Read MTZ test Entered testcase - Auto-read bad MTZ test got status: #() got status: #() PASS: Auto-read bad MTZ test Entered testcase - Map Sigma INFO:: map sigmas 0.311501026153564 #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 EntereINFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 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/_home_paule_data_greg-data_pdb1py3.ent_Sun_Sep__6_11:51:26_2015_modification_0.pdb.gz INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP INFO:: 25 residues had their atoms swapped INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 20 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.031 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.016 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.019 seconds for contour map INFO:: 0.07 seconds in total here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:26_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-pepflip-test.pdb PDB file /home/paule/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 22 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-pepflip-test.pdb_Sun_Sep__6_11:51:27_2015_modification_0.pdb.gz flipped 65 A INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 23 read successfully DEBUG:: there were 0 types with no dictionary in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x68df8a0 omega: 1 12.77 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_11:51:27_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_11:51:27_2015_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 flipped 11 A INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_11:51:27_2015_modification_2.pdb.gz created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 31 non-bonded restraints initial distortion_score: 2188 Initial RMS Z values bonds: 15.47 angles: 7.387 torsions: N/A planes: 6.517 non-bonded: 48.74 chiral vol: 3.045 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 74) at -4659 Final Estimated RMS Z Scores: bonds: 2.002 angles: 1.375 torsions: N/A planes: 3.303 non-bonded: 1.548 chiral vol: 0.06931 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.809 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.02 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_11:51:27_2015_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_11:51:27_2015_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_11:51:27_2015_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.448 created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 71 non-bonded restraints initial distortion_score: -5749 Initial RMS Z values bonds: 1.637 angles: 1.699 torsions: N/A planes: 4.83 non-bonded: 1.367 chiral vol: 0.5216 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 32) at -5912 Final Estimated RMS Z Scores: bonds: 1.796 angles: 1.21 torsions: N/A planes: 3.485 non-bonded: 0.6664 chiral vol: 0.1099 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 6.889 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.012 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_11:51:27_2015_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 24 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.032 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.026 seconds for contour map INFO:: 0.078 seconds in total created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 6 non-bonded restraints initial distortion_score: -2709 Initial RMS Z values bonds: 1.674 angles: 1.07 torsions: N/A planes: 1.965 non-bonded: 9.246 chiral vol: 1.462 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 10) at -2868 Final Estimated RMS Z Scores: bonds: 1.366 angles: 1.424 torsions: N/A planes: 2.035 non-bonded: 4.216 chiral vol: 0.6019 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.149 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.006 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:27_2015_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 26 read successfully DEBUG:: there were 0 types with no dictionary here in split_residue() DEBUG:: split_residue table 0 N :: INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_11:51:27_2015_modification_0.pdb.gz split_residue(int atom_index, int alt_conf_split_type) returns 0 debug:: split_residue() returned 0 "" created 20 bond restraints created 23 angle restraints created 0 plane restraints created 4 chiral vol restraints created 47 restraints Link restraints: 0 bond links 0 angle links 0 plane links 0 parallel plane restraints Flanking residue restraints: 5 bond links 15 angle links 10 plane links 0 parallel plane restraints INFO:: make_restraints(): made 784 non-bonded restraints initial distortion_score: -1.081e+04 Initial RMS Z values bonds: 1.806 angles: 0.8912 torsions: N/A planes: 2.122 non-bonded: 0.0008065 chiral vol: 0.669 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 36) at -1.102e+04 Final Estimated RMS Z Scores: bonds: 1.068 angles: 0.6751 torsions: N/A planes: 1.67 non-bonded: 0.00276 chiral vol: 0.2919 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.474 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_11:51:27_2015_modification_1.pdb.gz INFO:: replace_coords: 23 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it created 36 bond restraints created 40 angle restraints created 3 plane restraints created 5 chiral vol restraints created 84 restraints Link restraints: 4 bond links 12 angle links 8 plane links 0 parallel plane restraints Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 1031 non-bonded restraints initial distortion_score: -1.249e+04 Initial RMS Z values bonds: 0.9807 angles: 1.018 torsions: N/A planes: 9.549 non-bonded: 0.4795 chiral vol: 10.28 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 46) at -1.584e+04 Final Estimated RMS Z Scores: bonds: 1.681 angles: 1.892 torsions: N/A planes: 2.024 non-bonded: 0.005872 chiral vol: 1.841 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 7.725 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_11:51:27_2015_modification_2.pdb.gz INFO:: replace_coords: 41 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 27 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.03 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.019 seconds for contour map INFO:: 0.07 seconds in total created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -8536 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 45) at -1.157e+04 Final Estimated RMS Z Scores: bonds: 1.77 angles: 2.093 torsions: N/A planes: 2.225 non-bonded: 0.01872 chiral vol: 1.99 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.049 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.086 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: -426.5 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 51) at -2664 Final Estimated RMS Z Scores: bonds: 0.5488 angles: 1.686 torsions: N/A planes: 1.369 non-bonded: 0.008327 chiral vol: 1.322 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.216 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.167 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 470.7 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 67) at -1700 Final Estimated RMS Z Scores: bonds: 0.4278 angles: 1.637 torsions: N/A planes: 1.17 non-bonded: 0.006404 chiral vol: 1.276 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 8.429 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.212 created 29 bond restraints created 32 angle restraints created 2 plane restraints created 4 chiral vol restraints created 67 restraints INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A Link restraints: 3 bond links 9 angle links 6 plane links 0 parallel plane restraints INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links 0 parallel plane restraints INFO:: make_restraints(): made 315 non-bonded restraints initial distortion_score: 841.3 Initial RMS Z values bonds: 0.9358 angles: 1.058 torsions: N/A planes: 10.67 non-bonded: 0.7348 chiral vol: 11.48 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 32) at -1309 Final Estimated RMS Z Scores: bonds: 0.3693 angles: 1.616 torsions: N/A planes: 1.059 non-bonded: 0.005141 chiral vol: 1.304 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.077 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.648 INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-waters.pdb PDB file /home/paule/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 29 read successfully DEBUG:: there were 0 types with no dictionary masking....masking done INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-waters.pdb_Sun_Sep__6_11:51:29_2015_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it attempting to delete NULL moving_atoms_asc.mol ignoring INFO:: Reading coordinate file: /home/paule/data/greg-data/backrub-fragment.pdb PDB file /home/paule/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 30 read successfully DEBUG:: there were 0 types with no dictionary Symmetry available for this molecule INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Sun_Sep__6_11:51:29_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Sun_Sep__6_11:51:29_2015_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/coords-B3A.pdb PDB file /home/paule/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 32 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "B3A" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/b/B3A.cif created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 2.951 Initial RMS Z values bonds: 0.6619 angles: 0.3737 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.25 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 28) at 4.058e-05 Final Estimated RMS Z Scores: bonds: 0.0005327 angles: 0.002779 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0007482 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.711 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Sun_Sep__6_11:51:30_2015_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it WARNING: in init_refmac_mon_lib file "/home/paule/data/greg-data/lib-B3A.cif not found. init_refmac_mon_lib /home/paule/data/greg-data/lib-B3A.cif had no bond restraints created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 4.058e-05 Initial RMS Z values bonds: 0.0005327 angles: 0.002779 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0007482 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at 3.068e-05 Final Estimated RMS Z Scores: bonds: 0.0003435 angles: 0.00244 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0005781 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.801 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Sun_Sep__6_11:51:30_2015_modification_1.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it There are 3 data in /home/paule/data/greg-data/lib-both.cif Welcome to Coot created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: make_restraints(): made 5 non-bonded restraints initial distortion_score: 3.019 Initial RMS Z values bonds: 0.6708 angles: 0.3755 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.2535 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 30) at 3.942e-06 Final Estimated RMS Z Scores: bonds: 0.0005906 angles: 0.0006086 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.0005886 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 9.887 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Sun_Sep__6_11:51:30_2015_modification_2.pdb.gz INFO:: replace_coords: 6 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.033 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.018 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.018 seconds for contour map INFO:: 0.072 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. INFO:: Reading coordinate file: /home/paule/data/greg-data/test-TER-OXT.pdb PDB file /home/paule/data/greg-data/test-TER-OXT.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 34 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_test-TER-OXT.pdb_Sun_Sep__6_11:51:30_2015_modification_0.pdb.gz Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.13,-9.09,14.92) B-factor: 45 WARNING:: This residue already has an OXT - aborting INFO:: Reading coordinate file: /home/paule/data/greg-data/val.pdb PDB file /home/paule/data/greg-data/val.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 35 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_home_paule_data_greg-data_val.pdb_Sun_Sep__6_11:51:30_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/2yie-frag.pdb PDB file /home/paule/data/greg-data/2yie-frag.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 36 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_2yie-frag.pdb_Sun_Sep__6_11:51:30_2015_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04043 rms devi: 0.04717 max devi: 0.08328 min devi: 0.01301 INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 37 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NCO" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NCO.cif INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Sun_Sep__6_11:51:31_2015_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.04346 rms devi: 0.04779 max devi: 0.07399 min devi: 0.01477 INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb PDB file /home/paule/data/greg-data/4f8g.pdb has been read. Spacegroup: I 2 2 2 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 38 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Sun_Sep__6_11:51:31_2015_modification_0.pdb.gz INFO:: 6 matched atoms had: mean devi: 0.03945 rms devi: 0.04446 max devi: 0.06949 min devi: 0.01513 INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.032 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.018 seconds for FFT INFO:: 0.002 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.017 seconds for contour map INFO:: 0.069 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.03 seconds to read MTZ file INFO:: 0.035 seconds to initialize map INFO:: 0.042 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 1.22e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.052 Map minimum: ..... -0.9217 INFO:: 0.053 seconds for contour map INFO:: 0.168 seconds in total INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 41 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Masking around 64 atoms Map statistics: mean: -0.001403 st.d: 0.3056 Map statistics: min: -0.875, max: 2.978 -0.8269 9 -0.7306 46 -0.6343 403 -0.5379 2065 -0.4416 7564 -0.3453 17348 -0.249 26177 -0.1527 33633 -0.05636 40439 0.03995 41126 0.1363 21610 0.2326 10119 0.3289 5756 0.4252 4384 0.5215 3595 0.6178 3168 0.7142 2681 0.8105 2161 0.9068 1759 1.003 1314 1.099 958 1.196 645 1.292 455 1.388 271 1.485 175 1.581 108 1.677 59 1.774 34 1.87 17 1.966 7 2.063 2 2.159 1 2.255 4 2.352 1 2.448 0 2.544 1 2.64 0 2.737 0 2.833 0 2.929 1 3.026 0 d testcase - Hs are correctly swapped on a TYR results: (#t #t #t #t) PASS: Hs are correctly swapped on a TYR Entered testcase - Splitting residue leaves no atoms with negative occupancy PASS: Splitting residue leaves no atoms with negative occupancy Entered testcase - Pepflip flips the correct alt confed atoms PASS: Pepflip flips the correct alt confed atoms Entered testcase - Correction of CISPEP test CISPEPs: "3" PASS: Correction of CISPEP test Entered testcase - Refine Zone with Alt conf refined moved: d=0.301522740310835 PASS: Refine Zone with Alt conf Entered testcase - Sphere Refine ======= got bond length 1.29337076178799 PASS: Sphere Refine Entered testcase - Refinement gives useful results refinement results: ("" 0 (("Bonds" "Bonds: 1.770" 1.77012777328491) ("Angles" "Angles: 2.093" 2.09282064437866) ("Planes" "Planes: 2.225" 2.22537612915039) ("Non-bonded" "Non-bonded: 0.137" 0.136826604604721) ("Chirals" "Chirals: 1.990" 1.98961687088013))) ow factor: 2.01948535442352 INFO:: setting refinement weight to 14.7119362543797 refinement results: ("" 0 (("Bonds" "Bonds: 0.549" 0.548816204071045) ("Angles" "Angles: 1.686" 1.68625175952911) ("Planes" "Planes: 1.369" 1.3686261177063) ("Non-bonded" "Non-bonded: 0.091" 0.0912549123167992) ("Chirals" "Chirals: 1.322" 1.32221913337708))) ow factor: 1.23147830367088 INFO:: setting refinement weight to 9.70099536958725 refinement results: ("" 0 (("Bonds" "Bonds: 0.428" 0.427833080291748) ("Angles" "Angles: 1.637" 1.63654470443726) ("Planes" "Planes: 1.170" 1.16984879970551) ("Non-bonded" "Non-bonded: 0.080" 0.0800266414880753) ("Chirals" "Chirals: 1.276" 1.27565622329712))) ow factor: 1.12747070193291 INFO:: setting refinement weight to 7.63142727934291 refinement results: ("" 0 (("Bonds" "Bonds: 0.369" 0.369266390800476) ("Angles" "Angles: 1.616" 1.61552023887634) ("Planes" "Planes: 1.059" 1.05907106399536) ("Non-bonded" "Non-bonded: 0.072" 0.0716988444328308) ("Chirals" "Chirals: 1.304" 1.3041924238205))) ow factor: 1.08701252937317 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: (0.923012793064117 0.928160667419434 0.963148593902588 0.588746011257172 0.692066609859467 0.7519770860672 0.68085777759552 0.954908967018127 1.00084137916565 0.981854677200317 0.726146519184113) 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: -0.001403 st.d: 0.06012 Map statistics: min: -2.788, max: 0.7305 -2.744 1 -2.656 1 -2.568 1 -2.48 1 -2.392 1 -2.304 1 -2.217 0 -2.129 1 -2.041 0 -1.953 3 -1.865 1 -1.777 1 -1.689 5 -1.601 3 -1.513 4 -1.425 6 -1.337 21 -1.249 16 -1.161 41 -1.073 35 -0.9849 54 -0.897 68 -0.809 85 -0.721 108 -0.6331 116 -0.5451 145 -0.4571 148 -0.3692 181 -0.2812 209 -0.1932 264 -0.1052 356 -0.01728 223669 0.07069 639 0.1587 658 0.2466 505 0.3346 414 0.4226 223 0.5105 85 0.5985 22 0.6865 4 0.7744 0 diff-high-values: (0.00255920016206801 0.00100334209855646 0.0010665466543287 -0.00237780367024243 0.00169654528144747 7.12008564732969e-4 0.00212938035838306 0.00194926024414599 0.00229481048882008 6.55911106150597e-4 0.00835362635552883) diff-low-values: (-0.887997210025787 -0.793901443481445 -1.18933153152466 -1.06666207313538 -0.988452911376953 -0.759092748165131 -0.748683869838715 -0.650666236877441 -0.904519736766815 -0.545242071151733) INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.031 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.016 seconds for contour map INFO:: 0.067 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.034 seconds to read MTZ file INFO:: 0.086 seconds to initialize map INFO:: 0.059 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.131e-09 Map sigma: ....... 0.3115 Map maximum: ..... 3.071 Map minimum: ..... -0.8775 INFO:: 0.084 seconds for contour map INFO:: 0.273 seconds in total INFO:: multiplying map (function index) 0 Nuvw = ( 108, 132, 64) by 1 INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1 Map statistics: mean: -4.277e-07 st.d: 0.3111 Map statistics: min: -0.8734, max: 2.975 -0.8253 9 -0.7291 49 -0.6328 422 -0.5366 2147 -0.4404 7838 -0.3442 17838 -0.248 26781 -0.1518 34418 -0.05558 41152 0.04063 36651 0.1368 21808 0.233 10320 0.3293 5945 0.4255 4553 0.5217 3766 0.6179 3294 0.7141 2796 0.8103 2261 0.9065 1818 1.003 1374 1.099 984 1.195 684 1.291 472 1.388 284 1.484 182 1.58 106 1.676 63 1.772 39 1.869 15 1.965 10 2.061 2 2.157 2 2.253 5 2.35 2 2.446 1 2.542 2 2.638 1 2.735 0 2.831 1 2.927 1 3.023 0 Map statistics: mean: 4.288e-07 st.d: 0.001069 Map statistics: min: -0.006856, max: 0.01192 -0.006622 5 -0.006152 21 -0.005683 31 -0.005213 53 -0.004744 114 -0.004274 221 -0.003804 460 -0.003335 817 -0.002865 1522 -0.002396 2764 -0.001926 4797 -0.001457 9242 -0.0009874 19272 -0.0005178 40375 -4.832e-05 61229 0.0004212 44298 0.0008907 20928 0.00136 9475 0.00183 4783 0.002299 2778 0.002769 1679 0.003238 1172 0.003708 689 0.004177 491 0.004647 288 0.005116 198 0.005586 151 0.006055 102 0.006525 56 0.006995 37 0.007464 18 0.007934 10 0.008403 10 0.008873 3 0.009342 1 0.009812 3 0.01028 2 0.01075 0 0.01122 0 0.01169 0 0.01216 1 INFO:: Reading coordinate file: /home/paule/data/greg-data/multi-carbo-coot-2.pdb PDB file /home/paule/data/greg-data/multi-carbo-coot-2.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 48 read successfully DEBUG:: there were 2 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "FUC" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/f/FUC.cif INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAG.cif created 46 bond restraints created 82 angle restraints created 2 plane restraints created 8 chiral vol restraints created 138 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A INFO:: glycosidic_linkage type :ALPHA1-4: Link restraints: 1 bond links 3 angle links 0 plane links 0 parallel plane restraints INFO:: make_restraints(): made 671 non-bonded restraints initial distortion_score: 7037 Initial RMS Z values bonds: 11.36 angles: 3.259 torsions: N/A planes: 0.08353 non-bonded: 0.09438 chiral vol: 0.9035 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 397) at 0.7474 Final Estimated RMS Z Scores: bonds: 0.02236 angles: 0.09026 torsions: N/A planes: 0.001388 non-bonded: 2.091e-05 chiral vol: 0.04659 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 12.74 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 5 INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-2.pdb_Sun_Sep__6_11:51:33_2015_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-VAL.pdb PDB file /home/paule/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 49 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 80) at 0.2476 Final Estimated RMS Z Scores: bonds: 0.01102 angles: 0.09486 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1448 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 13.2 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_11:51:33_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: undo molecule number set to: 49 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_11:51:33_2015_modification_1.pdb.gz restoring from backup 2 2 INFO:: Reading coordinate file: coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_11:51:33_2015_modification_0.pdb.gz PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_11:51:33_2015_modification_0.pdb.gz has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: make_restraints(): made 44 non-bonded restraints initial distortion_score: 4.997 Initial RMS Z values bonds: 0.5425 angles: 0.1641 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.4516 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 80) at 0.2476 Final Estimated RMS Z Scores: bonds: 0.01102 angles: 0.09486 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1448 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 13.27 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_11:51:33_2015_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: Reading coordinate file: /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb PDB file /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 50 read successfully DEBUG:: there were 0 types with no dictionary created 17 bond restraints created 31 angle restraints created 0 plane restraints created 1 chiral vol restraints created 49 restraints INFO:: make_restraints(): made 67 non-bonded restraints initial distortion_score: 1137 Initial RMS Z values bonds: 5.621 angles: 3.433 torsions: N/A planes: N/A non-bonded: 3.491 chiral vol: 0.7534 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 260) at 0.4735 Final Estimated RMS Z Scores: bonds: 0.009656 angles: 0.1208 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 0.1385 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 13.82 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it debug:: restraints results 1 4 INFO:: backup file coot-backup/_home_paule_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Sun_Sep__6_11:51:34_2015_modification_0.pdb.gz INFO:: replace_coords: 18 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Symmetry available for this molecule created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 28 restraints INFO:: make_restraints(): made 39 non-bonded restraints initial distortion_score: 4023 Initial RMS Z values bonds: 1.152 angles: 0.8476 torsions: N/A planes: 3.056 non-bonded: 116.2 chiral vol: 0.7578 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 49) at -476.9 Final Estimated RMS Z Scores: bonds: 0.4635 angles: 0.3586 torsions: N/A planes: 0.3194 non-bonded: 0.02425 chiral vol: 0.04927 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 13.88 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.02 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_11:51:34_2015_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: make_restraints(): made 36 non-bonded restraints initial distortion_score: 3147 Initial RMS Z values bonds: 17.39 angles: 0.3586 torsions: N/A planes: 0.3194 non-bonded: 0 chiral vol: 0.04927 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -543.5 Final Estimated RMS Z Scores: bonds: 0.1298 angles: 0.1782 torsions: N/A planes: 0.4233 non-bonded: 0 chiral vol: 0.09974 rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 13.91 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.015 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_11:51:34_2015_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: wrote mmCIF "coot-test-ala.cif" INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 52 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "ACT" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ACT.cif There are 2 data in /home/paule/data/greg-data/libcheck_ACT.cif Welcome to Coot WARNING:: bond_restraint_length 4 should be 5 created 5 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 15 restraints INFO:: make_restraints(): made 7 non-bonded restraints initial distortion_score: 5304 Initial RMS Z values bonds: 0.01199 angles: 0.00654 torsions: N/A planes: 0 non-bonded: 755.8 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 2) at -138.3 Final Estimated RMS Z Scores: bonds: 0.0321 angles: 0.1906 torsions: N/A planes: 0.0364 non-bonded: 0 chiral vol: N/A rama plot: N/A start_pos: N/A GemanMcCl: N/A SUCCESS TIME:: (dragged refinement): 14.4 (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it Refinement elapsed time: 0.04 INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Sun_Sep__6_11:51:34_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. (process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 53 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_2.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_3.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_4.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_5.pdb.gz INFO:: Removing CIS peptide from PDB header: B 26 B 27 INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_6.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_7.pdb.gz Symmetry available for this molecule Symmetry available for this molecule INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:35_2015_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 56 read successfully DEBUG:: there were 0 types with no dictionary in new_molecule_by_residue_type_selection Something bad happened - No residues selected in new_molecule_by_residue_type_selection Something bad happened - No residues selected INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:36_2015_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 57 read successfully DEBUG:: there were 0 types with no dictionary INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%] INFO:: Reading coordinate file: /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 50/87 Molecule 58 read successfully DEBUG:: there were 0 types with no dictionary INFO:: aligning to mol number 58 chain: A ----- input to align_on_chain() ----------------- chain A target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID wgap -0.5 is_nucleic_acid_flag 0 console_output 1 --------------------------------------------------- INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID > target seq: DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 163.5 DEBUG:: s.length() 95 DEBUG:: nSelResidues 87 INFO:: backup file coot-backup/_home_paule_data_greg-data_rnase-A-needs-an-insertion.pdb_Sun_Sep__6_11:51:36_2015_modification_0.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 The alignment resulted in the following Insertions (coalesced): from 1 to 4 ASP VAL SER from 11 to 14 LEU PRO PRO from 62 to 64 PRO GLY Insertions (singles): [spec: 696 "A" 1 ""] -> ASP [spec: 696 "A" 2 ""] -> VAL [spec: 696 "A" 3 ""] -> SER [spec: 696 "A" 11 ""] -> LEU [spec: 696 "A" 12 ""] -> PRO [spec: 696 "A" 13 ""] -> PRO [spec: 696 "A" 62 ""] -> PRO [spec: 696 "A" 63 ""] -> GLY Deletions: [spec: 696 "A" 24 ""] [spec: 696 "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 59 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:37_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 60 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:37_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3hfl.ent PDB file /home/paule/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 61 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "PCA" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PCA.cif INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.025 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.013 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 8.67e-11 Map sigma: ....... 0.2604 Map maximum: ..... 1.718 Map minimum: ..... -1.034 INFO:: 0.009 seconds for contour map INFO:: 0.05 seconds in total INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Sun_Sep__6_11:51:38_2015_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.834 INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Sun_Sep__6_11:51:38_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.01207 rms devi: 0.01345 max devi: 0.02142 min devi: 0.003856 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1123 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.0847 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.01198 rms devi: 0.01335 max devi: 0.02126 min devi: 0.003873 INFO:: 5 matched atoms had: mean devi: 0.0002426 rms devi: 0.0002428 max devi: 0.0002567 min devi: 0.0002313 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08456 INFO:: 5 matched atoms had: mean devi: 0.2673 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1124 INFO:: 5 matched atoms had: mean devi: 6.931e-05 rms devi: 6.936e-05 max devi: 7.334e-05 min devi: 6.608e-05 INFO:: 5 matched atoms had: mean devi: 0.01203 rms devi: 0.01341 max devi: 0.02135 min devi: 0.003862 INFO:: 5 matched atoms had: mean devi: 0.0001386 rms devi: 0.0001387 max devi: 0.0001467 min devi: 0.0001322 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.01337 max devi: 0.02129 min devi: 0.003869 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.2703 rms devi: 0.3351 max devi: 0.5361 min devi: 0.08481 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Sun_Sep__6_11:51:38_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Sun_Sep__6_11:51:38_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.3372 max devi: 0.5475 min devi: 0.08176 INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 INFO:: 5 matched atoms had: mean devi: 0.01207 rms devi: 0.01345 max devi: 0.02142 min devi: 0.003856 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08463 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1123 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.0847 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.01198 rms devi: 0.01335 max devi: 0.02126 min devi: 0.003873 INFO:: 5 matched atoms had: mean devi: 0.0002426 rms devi: 0.0002428 max devi: 0.0002567 min devi: 0.0002313 INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.335 max devi: 0.536 min devi: 0.08456 INFO:: 5 matched atoms had: mean devi: 0.2673 rms devi: 0.3228 max devi: 0.4951 min devi: 0.1124 INFO:: 5 matched atoms had: mean devi: 6.931e-05 rms devi: 6.936e-05 max devi: 7.334e-05 min devi: 6.608e-05 INFO:: 5 matched atoms had: mean devi: 0.01203 rms devi: 0.01341 max devi: 0.02135 min devi: 0.003862 INFO:: 5 matched atoms had: mean devi: 0.0001386 rms devi: 0.0001387 max devi: 0.0001467 min devi: 0.0001322 INFO:: 5 matched atoms had: mean devi: 0.012 rms devi: 0.01337 max devi: 0.02129 min devi: 0.003869 INFO:: 5 matched atoms had: mean devi: 0.2674 rms devi: 0.3228 max devi: 0.4952 min devi: 0.1122 INFO:: 5 matched atoms had: mean devi: 0.2703 rms devi: 0.3351 max devi: 0.5361 min devi: 0.08481 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Sun_Sep__6_11:51:38_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-RNA_Sun_Sep__6_11:51:38_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269 rms devi: 0.3372 max devi: 0.5475 min devi: 0.08176 INFO:: 5 matched atoms had: mean devi: 0.005899 rms devi: 0.00671 max devi: 0.01013 min devi: 0.002581 INFO:: 5 matched atoms had: mean devi: 0.007256 rms devi: 0.007788 max devi: 0.01256 min devi: 0.00456 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08783 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5339 min devi: 0.0879 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.007179 rms devi: 0.0077 max devi: 0.01241 min devi: 0.004575 INFO:: 5 matched atoms had: mean devi: 0.005744 rms devi: 0.006571 max devi: 0.009959 min devi: 0.002425 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08776 INFO:: 5 matched atoms had: mean devi: 0.2677 rms devi: 0.3265 max devi: 0.5055 min devi: 0.1047 INFO:: 5 matched atoms had: mean devi: 0.005854 rms devi: 0.006669 max devi: 0.01008 min devi: 0.002535 INFO:: 5 matched atoms had: mean devi: 0.007225 rms devi: 0.007753 max devi: 0.0125 min devi: 0.004565 INFO:: 5 matched atoms had: mean devi: 0.00581 rms devi: 0.006629 max devi: 0.01003 min devi: 0.00249 INFO:: 5 matched atoms had: mean devi: 0.007194 rms devi: 0.007718 max devi: 0.01244 min devi: 0.004572 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3266 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3365 max devi: 0.5339 min devi: 0.08801 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.09235 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004329 rms devi: 0.004818 max devi: 0.007383 min devi: 0.001862 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.326 max devi: 0.5019 min devi: 0.09266 INFO:: 5 matched atoms had: mean devi: 0.005899 rms devi: 0.00671 max devi: 0.01013 min devi: 0.002581 INFO:: 5 matched atoms had: mean devi: 0.007256 rms devi: 0.007788 max devi: 0.01256 min devi: 0.00456 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08783 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1046 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5339 min devi: 0.0879 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3265 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.007179 rms devi: 0.0077 max devi: 0.01241 min devi: 0.004575 INFO:: 5 matched atoms had: mean devi: 0.005744 rms devi: 0.006571 max devi: 0.009959 min devi: 0.002425 INFO:: 5 matched atoms had: mean devi: 0.2718 rms devi: 0.3364 max devi: 0.5338 min devi: 0.08776 INFO:: 5 matched atoms had: mean devi: 0.2677 rms devi: 0.3265 max devi: 0.5055 min devi: 0.1047 INFO:: 5 matched atoms had: mean devi: 0.005854 rms devi: 0.006669 max devi: 0.01008 min devi: 0.002535 INFO:: 5 matched atoms had: mean devi: 0.007225 rms devi: 0.007753 max devi: 0.0125 min devi: 0.004565 INFO:: 5 matched atoms had: mean devi: 0.00581 rms devi: 0.006629 max devi: 0.01003 min devi: 0.00249 INFO:: 5 matched atoms had: mean devi: 0.007194 rms devi: 0.007718 max devi: 0.01244 min devi: 0.004572 INFO:: 5 matched atoms had: mean devi: 0.2678 rms devi: 0.3266 max devi: 0.5056 min devi: 0.1045 INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3365 max devi: 0.5339 min devi: 0.08801 !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_0.pdb.gz INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2702 rms devi: 0.3364 max devi: 0.5384 min devi: 0.0854 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2719 rms devi: 0.3363 max devi: 0.5345 min devi: 0.09235 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.004329 rms devi: 0.004818 max devi: 0.007383 min devi: 0.001862 INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_11:51:38_2015_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.2657 rms devi: 0.326 max devi: 0.5019 min devi: 0.09266 Symmetry available for this molecule INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:38_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/some-waters-with-ter.pdb PDB file /home/paule/data/greg-data/some-waters-with-ter.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 68 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_some-waters-with-ter.pdb_Sun_Sep__6_11:51:38_2015_modification_0.pdb.gz 1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/tm+some-waters.pdb PDB file /home/paule/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 69 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3115 INFO:: Using density cut-off: 0.623 (2 sigma) (mean -0.0337 stdev: 0.1461) 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 = ( 59.91, 3.027, -4.296) is too big to be water INFO:: cluster at xyz = ( 70.01, 19.05, 18.63) is too big to be water INFO:: found 45 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_tm+some-waters.pdb_Sun_Sep__6_11:51:39_2015_modification_0.pdb.gz INFO:: Adding to solvent chain: D INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 70 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_0.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_1.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_2.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_3.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_4.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_5.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_6.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_7.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_8.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_9.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_10.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_11.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_12.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_13.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_14.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_15.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_16.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_17.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_18.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_19.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_20.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_21.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_22.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_23.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_24.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_25.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_26.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_27.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_28.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_29.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_30.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_31.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_32.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_33.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_34.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_35.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_36.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_37.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_38.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_39.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_40.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_41.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_42.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_43.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_44.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_45.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_46.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_47.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_48.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_49.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_50.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_51.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_52.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_53.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_54.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_55.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_56.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_57.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_58.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_59.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_60.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_61.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_62.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_63.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_64.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_65.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_66.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_67.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_68.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_69.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_70.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_71.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_72.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_73.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_74.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_75.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_76.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_77.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_78.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_79.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_80.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_81.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_82.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_83.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_84.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_85.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_86.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_87.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_88.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_89.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_90.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_91.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_92.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_93.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_94.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_95.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_96.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_97.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_98.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:39_2015_modification_99.pdb.gz 0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/water-test-no-cell.pdb PDB file /home/paule/data/greg-data/water-test-no-cell.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 71 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_water-test-no-cell.pdb_Sun_Sep__6_11:51:42_2015_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules INFO:: Reading coordinate file: /home/paule/data/greg-data/pathological-water-test.pdb PDB file /home/paule/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 72 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_pathological-water-test.pdb_Sun_Sep__6_11:51:43_2015_modification_0.pdb.gz INFO:: moved 181 water molecules Symmetry available for this molecule INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.03 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.017 seconds for FFT INFO:: 0.003 seconds for statistics Map mean: ........ 1.054e-09 Map sigma: ....... 0.3115 Map maximum: ..... 2.978 Map minimum: ..... -0.875 INFO:: 0.02 seconds for contour map INFO:: 0.071 seconds in total INFO:: Masking around 58 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. A 94 ALA N :: xyz = ( 58.42, 2.762, -2.12) A 94 ALA C :: xyz = ( 60.22, 2.538, -3.781) A 94 ALA CA :: xyz = ( 59.68, 2.109, -2.419) A 94 ALA O :: xyz = ( 61.35, 3.018, -3.893) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:43_2015_modification_0.pdb.gz Symmetry available for this molecule DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 75 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 75 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.179 rms devi: 4.859 max devi: 46.26 min devi: 0.1254 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:43_2015_modification_0.pdb.gz PASS: Mask and difference map Entered testcase - Simple Averaged maps INFO:: map sigmas: normal 0.311072021722794 and diff-map: 0.00106883328408003 PASS: Simple Averaged maps Entered testcase - Make a glycosidic linkage bond-length: 2.97694066606539: bond-length: 1.44034108558188: PASS: Make a glycosidic linkage Entered testcase - Test for flying hydrogens on undo PASS: Test for flying hydrogens on undo Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0 PASS: Test for mangling of hydrogen names from a PDB v 3.0 Entered testcase - correct matching dictionary names from test name PASS: correct matching dictionary names from test name Entered testcase - update monomer restraints Bond-length: 2.83654792022318: pass intermediate 2.8 tolerance test OK plane atom " CB " Bond-length: 1.51583112178846: PASS: update monomer restraints Entered testcase - Write mmCIF restraints correctly PASS: Write mmCIF restraints correctly Entered testcase - Refinement OK with zero bond esd PASS: Refinement OK with zero bond esd Entered testcase - Change Chain IDs and Chain Sorting PASS: Change Chain IDs and Chain Sorting Entered testcase - Replace Fragment distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) PASS: Replace Fragment Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () PASS: Residues in Region of Residue Entered testcase - Residues in region of a point PASS: Residues in region of a point Entered testcase - Empty molecule on type selection PASS: Empty molecule on type selection Entered testcase - Set Rotamer PASS: Set Rotamer Entered testcase - Rotamer names and scores are correct Rotamer 0 : "m-85" 100.0 Rotamer 1 : "t80" 90.1668395996094 Rotamer 2 : "p90" 50.7077865600586 Rotamer 3 : "m -30 " 21.4231548309326 Rotamer 4 : "m -30 " 21.4231548309326 PASS: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions ::::: (58 "A" 1 "") #f #f ::::: (58 "A" 4 "") #t #t ::::: (58 "A" 59 "") #t #t ::::: (58 "A" 60 "") #f #f ::::: (58 "A" 61 "") #f #f ::::: (58 "A" 92 "") #t #t ::::: (58 "A" 94 "") #f #f PASS: Align and mutate a model with deletions Entered testcase - renumbered residues should be in seqnum order PASS: renumbered residues should be in seqnum order Entered testcase - Autofit Rotamer on Residues with Insertion codes PASS: Autofit Rotamer on Residues with Insertion codes Entered testcase - RNA base has correct residue type after mutation mutated base to type "C" - was "A" mutated base to type "Cr" - was "A" PASS: RNA base has correct residue type after mutation Entered testcase - resname from serial number doesnt crash on silly input PASS: resname from serial number doesnt crash on silly input Entered testcase - DNA bases are the correct residue type after mutation mutated base to type "DC" mutated base to type "DG" mutated base to type "DA" mutated base to type "DT" mutated base to type "Cd" mutated base to type "Gd" mutated base to type "Ad" mutated base to type "Td" PASS: DNA bases are the correct residue type after mutation Entered testcase - SegIDs are correct after mutate PASS: SegIDs are correct after mutate Entered testcase - TER on water chain is removed on adding a water by hand PASS: TER on water chain is removed on adding a water by hand Entered testcase - TER on water chain is removed on adding waters automatically PASS: TER on water chain is removed on adding waters automatically Entered testcase - Adding atoms to Many-Chained Molecule PASS: Adding atoms to Many-Chained Molecule Entered testcase - Arrange waters round protein PASS: Arrange waters round protein Entered testcase - Correct Segid After Add Terminal Residue PASS: Correct Segid After Add Terminal Residue Entered testcase - Correct Segid after NCS residue range copy PASS: Correct Segid after NCS residue range copy Entered testcase - Merge WaterINFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 76 read successfully DEBUG:: there were 0 types with no dictionary 0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule (and new chain) 1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.6,8.687,12.91) B-factor: 45 added to molecule 1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.6,8.687,12.91) B-factor: 45 added to molecule 1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.6,8.687,12.91) B-factor: 45 added to molecule 1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.6,8.687,12.91) B-factor: 45 added to molecule 1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.6,8.687,12.91) B-factor: 45 added to molecule 1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.6,8.687,12.91) B-factor: 45 added to molecule 1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.6,8.687,12.91) B-factor: 45 added to molecule 1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.6,8.687,12.91) B-factor: 45 added to molecule 1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.6,8.687,12.91) B-factor: 45 added to molecule 1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.6,8.687,12.91) B-factor: 45 added to molecule 1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.6,8.687,12.91) B-factor: 45 added to molecule 1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.6,8.687,12.91) B-factor: 45 added to molecule 1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.6,8.687,12.91) B-factor: 45 added to molecule 1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.6,8.687,12.91) B-factor: 45 added to molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 77 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "TAR" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TAR.cif INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 78 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 79 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "NPO" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NPO.cif -X,-X+Y,-Z+1/3 -> -1 0 0 -1 1 0 0 0 -1 translations: 0 0 0.3333 pre-trans: 0 0 0 Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule INFO:: Matching/moving molecule number 82 to 81 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.03532 rms devi: 0.03779 max devi: 0.05453 min devi: 0.01668 INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076) INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:45_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 83 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent PDB file /home/paule/data/greg-data/pdb1py3.ent has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 91/204 INFO:: NCS chain comparison 90/204 INFO:: NCS chain comparison 175/179 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain B" Molecule 84 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 83 to 84 INFO:: LSQ matched 164 atoms INFO:: 164 matched atoms had: mean devi: 0.5023 rms devi: 0.5938 max devi: 1.679 min devi: 0.04318 INFO:: Axis orientation: ( 0.567, -0.7175, 0.4046) INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019) INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:46_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.8273, 0.1661, 0.5366| | -0.3732, 0.8765, 0.3041| | -0.4199, -0.4519, 0.7871| ( 33.77, -3.902, -16.53) INFO:: fractional coordinates matrix: | 0.8273, 0.2005, 0.3208| | -0.3092, 0.8765, 0.1506| | -0.7024, -0.9123, 0.7871| ( 0.5204, -0.04982, -0.426) INFO:: spacegroup: C 1 2 1 INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 85 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:51:46_2015_modification_0.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 86 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Reading coordinate file: /home/paule/data/greg-data/2goz-manip.pdb PDB file /home/paule/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 INFO:: Found 1 models Model 1 had 7 links Symmetry available for this molecule INFO:: NCS chain comparison 10/85 Molecule 87 read successfully DEBUG:: there were 7 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "GDP" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GDP.cif INFO:: using standard CCP4 Refmac dictionary to search for "Gr" INFO:: using standard CCP4 Refmac dictionary to search for "Ar" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif INFO:: using standard CCP4 Refmac dictionary to search for "Ur" INFO:: using standard CCP4 Refmac dictionary to search for "Cr" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif INFO:: using standard CCP4 Refmac dictionary to search for "OMC" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/o/OMC.cif INFO:: using standard CCP4 Refmac dictionary to search for "5BU" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/5/5BU.cif SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.903 13.7 9.237 90 98.21 90 READ-INS:: Spacegroup: "P 1 21/c 1" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 88 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.32 34.32 11.09 90 90 90 READ-INS:: Spacegroup: "I 41 2 2" INFO:: chain has 2 residues Symmetry available for this molecule Molecule 89 read successfully INFO:: spacegroup: I 41 2 2 LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.73 77.73 77.73 90 90 90 READ-INS:: Spacegroup: "I 21 3" INFO:: chain has 121 residues Symmetry available for this molecule Molecule 90 read successfully ll: 24 DEBUG:: space group initialised with symbol "I 21 3" in read_data_sm_cif() cell is Cell (77.726,77.726,77.726, 90, 90, 90) in read_data_sm_cif() spg is I 21 3 in read_data_sm_cif() reso is 0.5889 Map statistics: mean: -5.07e-05 st.d: 0.3052 Map statistics: min: -0.781, max: 6.079 -0.6953 231 -0.5238 4724 -0.3523 24910 -0.1808 55291 -0.00927 95241 0.1622 40930 0.3337 7480 0.5052 3968 0.6767 2790 0.8482 2117 1.02 1738 1.191 1221 1.363 888 1.534 595 1.706 355 1.877 240 2.049 137 2.22 97 2.392 62 2.563 46 2.735 17 2.906 17 3.078 13 3.249 10 3.421 7 3.592 1 3.764 3 3.935 7 4.107 2 4.278 5 4.45 1 4.621 2 4.793 2 4.964 0 5.136 1 5.307 0 5.479 0 5.65 0 5.822 0 5.993 1 6.165 0 Map statistics: mean: -1.005e-05 st.d: 0.04681 Map statistics: min: -0.2115, max: 0.6486 -0.2008 7 -0.1793 48 -0.1578 209 -0.1363 787 -0.1148 2257 -0.09325 5676 -0.07175 12730 -0.05025 24380 -0.02874 38191 -0.007239 46229 0.01427 43880 0.03577 32484 0.05727 19420 0.07878 9718 0.1003 4120 0.1218 1677 0.1433 718 0.1648 329 0.1863 133 0.2078 77 0.2293 29 0.2508 11 0.2723 13 0.2938 8 0.3153 2 0.3368 2 0.3583 2 0.3798 1 0.4013 1 0.4228 2 0.4443 2 0.4658 1 0.4873 1 0.5088 1 0.5304 1 0.5519 1 0.5734 0 0.5949 0 0.6164 0 0.6379 2 0.6594 0 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 WARNING:: invalid molecule (204050) for write_shelx_ins_file WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2" WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C " WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N " WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA " INFO:: SHELXL file rnase.ins written. Chains PASS: Merge Water Chains Entered testcase - Consolidated merge -------- starting chain list ----------- DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "") DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K") PASS: Consolidated merge Entered testcase - LSQ by atom PASS: LSQ by atom Entered testcase - LSQing changes the space-group and cell to that of the reference molecule PASS: LSQing changes the space-group and cell to that of the reference molecule Entered testcase - set-residue-name sets the correct residue PASS: set-residue-name sets the correct residue Entered testcase - fit-protein-make-specs makes all specs specs: 189 ((86 "A" 1 "") (86 "A" 2 "") (86 "A" 3 "") (86 "A" 4 "") (86 "A" 5 "") (86 "A" 6 "") (86 "A" 7 "") (86 "A" 8 "") (86 "A" 9 "") (86 "A" 10 "") (86 "A" 11 "") (86 "A" 12 "") (86 "A" 13 "") (86 "A" 14 "") (86 "A" 15 "") (86 "A" 16 "") (86 "A" 17 "") (86 "A" 18 "") (86 "A" 19 "") (86 "A" 20 "") (86 "A" 21 "") (86 "A" 22 "") (86 "A" 23 "") (86 "A" 24 "") (86 "A" 25 "") (86 "A" 26 "") (86 "A" 27 "") (86 "A" 28 "") (86 "A" 29 "") (86 "A" 30 "") (86 "A" 31 "") (86 "A" 32 "") (86 "A" 33 "") (86 "A" 34 "") (86 "A" 35 "") (86 "A" 36 "") (86 "A" 37 "") (86 "A" 38 "") (86 "A" 39 "") (86 "A" 40 "") (86 "A" 41 "") (86 "A" 42 "") (86 "A" 43 "") (86 "A" 44 "") (86 "A" 45 "") (86 "A" 46 "") (86 "A" 47 "") (86 "A" 48 "") (86 "A" 49 "") (86 "A" 50 "") (86 "A" 51 "") (86 "A" 52 "") (86 "A" 53 "") (86 "A" 54 "") (86 "A" 55 "") (86 "A" 56 "") (86 "A" 57 "") (86 "A" 58 "") (86 "A" 59 "") (86 "A" 60 "") (86 "A" 61 "") (86 "A" 62 "") (86 "A" 63 "") (86 "A" 64 "") (86 "A" 65 "") (86 "A" 66 "") (86 "A" 67 "") (86 "A" 68 "") (86 "A" 69 "") (86 "A" 70 "") (86 "A" 71 "") (86 "A" 72 "") (86 "A" 73 "") (86 "A" 74 "") (86 "A" 75 "") (86 "A" 76 "") (86 "A" 77 "") (86 "A" 78 "") (86 "A" 79 "") (86 "A" 80 "") (86 "A" 81 "") (86 "A" 82 "") (86 "A" 83 "") (86 "A" 84 "") (86 "A" 85 "") (86 "A" 86 "") (86 "A" 87 "") (86 "A" 88 "") (86 "A" 89 "") (86 "A" 90 "") (86 "A" 91 "") (86 "A" 92 "") (86 "A" 93 "") (86 "B" 1 "") (86 "B" 2 "") (86 "B" 3 "") (86 "B" 4 "") (86 "B" 5 "") (86 "B" 6 "") (86 "B" 7 "") (86 "B" 8 "") (86 "B" 9 "") (86 "B" 10 "") (86 "B" 11 "") (86 "B" 12 "") (86 "B" 13 "") (86 "B" 14 "") (86 "B" 15 "") (86 "B" 16 "") (86 "B" 17 "") (86 "B" 18 "") (86 "B" 19 "") (86 "B" 20 "") (86 "B" 21 "") (86 "B" 22 "") (86 "B" 23 "") (86 "B" 24 "") (86 "B" 25 "") (86 "B" 26 "") (86 "B" 27 "") (86 "B" 28 "") (86 "B" 29 "") (86 "B" 30 "") (86 "B" 31 "") (86 "B" 32 "") (86 "B" 33 "") (86 "B" 34 "") (86 "B" 35 "") (86 "B" 36 "") (86 "B" 37 "") (86 "B" 38 "") (86 "B" 39 "") (86 "B" 40 "") (86 "B" 41 "") (86 "B" 42 "") (86 "B" 43 "") (86 "B" 44 "") (86 "B" 45 "") (86 "B" 46 "") (86 "B" 47 "") (86 "B" 48 "") (86 "B" 49 "") (86 "B" 50 "") (86 "B" 51 "") (86 "B" 52 "") (86 "B" 53 "") (86 "B" 54 "") (86 "B" 55 "") (86 "B" 56 "") (86 "B" 57 "") (86 "B" 58 "") (86 "B" 59 "") (86 "B" 60 "") (86 "B" 61 "") (86 "B" 62 "") (86 "B" 63 "") (86 "B" 64 "") (86 "B" 65 "") (86 "B" 66 "") (86 "B" 67 "") (86 "B" 68 "") (86 "B" 69 "") (86 "B" 70 "") (86 "B" 71 "") (86 "B" 72 "") (86 "B" 73 "") (86 "B" 74 "") (86 "B" 75 "") (86 "B" 76 "") (86 "B" 77 "") (86 "B" 78 "") (86 "B" 79 "") (86 "B" 80 "") (86 "B" 81 "") (86 "B" 82 "") (86 "B" 83 "") (86 "B" 84 "") (86 "B" 85 "") (86 "B" 86 "") (86 "B" 87 "") (86 "B" 88 "") (86 "B" 89 "") (86 "B" 90 "") (86 "B" 91 "") (86 "B" 92 "") (86 "B" 93 "") (86 "B" 94 "") (86 "B" 95 "") (86 "B" 96 "")) PASS: fit-protein-make-specs makes all specs Entered testcase - Phosphate distance in pucker analysis is sane PASS: Phosphate distance in pucker analysis is sane Ended 01-pdb+mtz.scm Running 02-shelx.scm ... Entered testcase - Read small molecule .res file PASS: Read small molecule .res file Entered testcase - Read hollander small molecule .res file PASS: Read hollander small molecule .res file Entered testcase - read shelx insulin with fcf PASS: read shelx insulin with fcf Entered testcase - Write an INS from PDB test PASS: Write an INS from PDB test Entered testcase - new molecule by atom selection inheritsSymmetry available for this molecule Symmetry available for this molecule INFO:: Masking around 32 atoms fitting terminal residue with 100 random trials INFO:: Fitting terminal residue without individual rigid body fitting. B 2021 ALA N :: xyz = ( -11.33, 19.47, 57.91) B 2021 ALA C :: xyz = ( -12.04, 20.27, 60.12) B 2021 ALA CA :: xyz = ( -11.37, 20.62, 58.8) B 2021 ALA O :: xyz = ( -11.44, 20.43, 61.19) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Sun_Sep__6_11:51:48_2015_modification_0.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 2010 "HIS" " N " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CA " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " C " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " O " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CB " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CG " WARNING:: failed to get AFIX handle for "" 2010 "HIS" " ND1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CE1" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " NE2" WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CD2" INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Sun_Sep__6_11:51:48_2015_modification_0.res 1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.3052 INFO:: Using density cut-off: 0.1831 (0.6 sigma) (mean -0.02035 stdev: 0.1119) INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters. INFO:: Using water to protein distance limits: 2.4 3.2 INFO:: Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water INFO:: found 28 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Sun_Sep__6_11:51:48_2015_modification_1.res ERROR transfering AFIX back WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O " INFO:: Adding to solvent chain: D LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.14 83.03 89.79 90 90 90 READ-INS:: Spacegroup: "P 21 21 21" INFO:: chain has 5 residues Symmetry available for this molecule Molecule 95 read successfully LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.7 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 96 read successfully INFO:: SHELXL file new-horma.ins written. LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.7 90 READ-INS:: Spacegroup: "P 1 21 1" INFO:: chain has 23 residues Symmetry available for this molecule Molecule 97 read successfully LATT LINE: LATT -2 SFAC LINE: SFAC S INFO:: CELL set to 109 109 107.6 90 90 90 READ-INS:: Spacegroup: "I 4 2 2" INFO:: chain has 4 residues Symmetry available for this molecule Molecule 98 read successfully INFO:: Creating directory coot-ccp4 shelx molecule flag PASS: new molecule by atom selection inherits shelx molecule flag Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy Entered testcase - Add water to SHELX molecule PASS: Add water to SHELX molecule Entered testcase - Find Waters for a SHELXL molecule PASS: Find Waters for a SHELXL molecule Entered testcase - NPD Anisotropic Atom [Mitch Miller] PASS: NPD Anisotropic Atom [Mitch Miller] Entered testcase - close shelx molecules PASS: close shelx molecules Entered testcase - Aniso Bs in P21 b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) PASS: Aniso Bs in P21 Entered testcase - Don't crash on reading a strange HAT file PASS: Don't crash on reading a strange HAT file Ended 02-shelx.scm Running 03-ligand.scm ... Entered testcase - Get monomer test run-command-in-dir dir: "coot-ccp4/" exe: "libcheck" cl-args: () data-lines: ("N" "MON 3GP" "") log-file-name: "coot-libcheck-3GP.log" #t : : --- LIBCHECK --- /Vers 5.2.00 ; 12.12.2011/ : : : 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 : NUMBER OF MONOMERS IN THE LIBRARY : 11459 : with complete description : 11459 : NUMBER OF MODIFICATIONS : 53 : NUMBER OF LINKS : 66 : I am reading libraries. Please wait. : - energy parameters : - monomer"s description (links & mod ) : I am reading library. Please wait. : - monomer"s description : * 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 6.3: Refmac_5.7.0029     version 5.7.0029 : 25/06/12##
: ###############################################################
: User: unknown  Run date:  6/ 9/2015 Run time: 11:51:52 
:
:
: Please reference: Collaborative Computational Project, Number 4. 1994.
: "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
: 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 : /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /home/paule/ccp4/ccp4-6.3.0/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
:  NUMBER OF MONOMERS IN THE LIBRARY          : 11459
:                with complete description    : 11459
:  NUMBER OF MODIFICATIONS                    :    53
:  NUMBER OF LINKS                            :    66
:  I am reading libraries. Please wait.
:      - energy parameters
:      - monomer"s description (links & mod )
:
:FORMATTED      OLD     file opened on unit  45
:
:Logical name: ATOMSF, Filename: /home/paule/ccp4/ccp4-6.3.0/lib/data/atomsf.lib
:
:
:
: Spacegroup information obtained from library file: 
: Logical Name: SYMINFO   Filename: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/share/coot/syminfo.lib
:
:  WARNING: "SCALE" card is absent in input PDB file
:  Number of atoms    :      36
:  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           :       0
:  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:        38         0        38
:               Angles:        66         0        66
:              Chirals:         4         0         4
:               Planes:         2         0         2
:             Torsions:        22         0        22
:---------------------------------------
:
:
:
:     CGMAT cycle number =      1
:
: function value    19446.4160    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.030     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     4.292     3.000
:Bond angles  : others                            26     1.222     3.000
:Torsion angles, period  1. refined               15     3.618    15.000
:Torsion angles, period  1. others                 3     0.015    15.000
:Torsion angles, period  3. refined                4     5.039    15.000
: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                             6     0.189     0.200
:VDW; torsion: refined_atoms                       7     0.281     0.200
:VDW; torsion.others                               4     0.224     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.00000000    
: Not converging with gamma equal    0.00000000    
: Trying gamma equal    5.50000034E-02
: Gamma decreased to    4.40000035E-02
:
:
: fvalues    0.00000000       19446.4160       363.927856       19446.4160    
:
:
:     CGMAT cycle number =      2
:
: function value    363.927856    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.081     0.020
:Bond distances: others                           12     0.013     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    4.40000035E-02
: Gamma decreased to    3.40000018E-02
:
:
: fvalues    0.00000000       363.927856       1259.59216       363.927856    
:
: fvalues    0.00000000       363.927856       483.191711       363.927856    
:
:
:     CGMAT cycle number =      3
:
: function value    343.507812    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.079     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    3.40000018E-02
: Gamma decreased to    2.49090921E-02
:
:
: fvalues    0.00000000       343.507812       293.110168       343.507812    
:
:
:     CGMAT cycle number =      4
:
: function value    293.110168    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.076     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    2.49090921E-02
: Gamma decreased to    1.66446306E-02
:
:
: fvalues    0.00000000       293.110168       287.582001       293.110168    
:
:
:     CGMAT cycle number =      5
:
: function value    287.582001    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    1.66446306E-02
: Gamma decreased to    9.13148280E-03
:
:
: fvalues    0.00000000       287.582001       230.526413       287.582001    
:
:
:     CGMAT cycle number =      6
:
: function value    230.526413    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    9.13148280E-03
: Not converging with gamma equal    9.13148280E-03
: Trying gamma equal    4.66972217E-02
: Gamma decreased to    3.91840748E-02
:
:
: fvalues    0.00000000       230.526413       281.710724       230.526413    
:
: fvalues    0.00000000       230.526413       242.137283       230.526413    
:
:
:     CGMAT cycle number =      7
:
: function value    233.002716    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    3.91840748E-02
: Gamma decreased to    3.23539414E-02
:
:
: fvalues    0.00000000       233.002716       230.082397       233.002716    
:
:
:     CGMAT cycle number =      8
:
: function value    230.082397    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    3.23539414E-02
: Gamma decreased to    2.61447281E-02
:
:
: fvalues    0.00000000       230.082397       229.981308       230.082397    
:
:
:     CGMAT cycle number =      9
:
: function value    229.981308    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    2.61447281E-02
: Gamma decreased to    2.04999894E-02
:
:
: fvalues    0.00000000       229.981308       229.512283       229.981308    
:
:
:     CGMAT cycle number =     10
:
: function value    229.512283    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    2.04999894E-02
: Not converging with gamma equal    2.04999894E-02
: Trying gamma equal    4.87236828E-02
: Not converging with gamma equal    4.87236828E-02
: Trying gamma equal    7.97697455E-02
: Not converging with gamma equal    7.97697455E-02
: Trying gamma equal   0.113920420    
: Not converging with gamma equal   0.113920420    
: Trying gamma equal   0.151486158    
: Not converging with gamma equal   0.151486158    
: Trying gamma equal   0.192808479    
: Gamma decreased to   0.184544012    
:
:
: fvalues    0.00000000       229.512283       229.479935       229.512283    
:
:
:     CGMAT cycle number =     11
:
: function value    229.479935    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.184544012    
: Gamma decreased to   0.177030861    
:
:
: fvalues    0.00000000       229.479935       229.449692       229.479935    
:
:
:     CGMAT cycle number =     12
:
: function value    229.449692    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.177030861    
: Gamma decreased to   0.170200720    
:
:
: fvalues    0.00000000       229.449692       229.420837       229.449692    
:
:
:     CGMAT cycle number =     13
:
: function value    229.420837    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.170200720    
: Gamma decreased to   0.163991511    
:
:
: fvalues    0.00000000       229.420837       229.393265       229.420837    
:
:
:     CGMAT cycle number =     14
:
: function value    229.393265    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.163991511    
: Gamma decreased to   0.158346772    
:
:
: fvalues    0.00000000       229.393265       229.366852       229.393265    
:
:
:     CGMAT cycle number =     15
:
: function value    229.366852    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.158346772    
: Gamma decreased to   0.153215185    
:
:
: fvalues    0.00000000       229.366852       229.341660       229.366852    
:
:
:     CGMAT cycle number =     16
:
: function value    229.341660    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.153215185    
: Gamma decreased to   0.148550108    
:
:
: fvalues    0.00000000       229.341660       229.317780       229.341660    
:
:
:     CGMAT cycle number =     17
:
: function value    229.317780    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.148550108    
: Gamma decreased to   0.144309133    
:
:
: fvalues    0.00000000       229.317780       229.295120       229.317780    
:
:
:     CGMAT cycle number =     18
:
: function value    229.295120    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.144309133    
: Gamma decreased to   0.140453696    
:
:
: fvalues    0.00000000       229.295120       229.273788       229.295120    
:
:
:     CGMAT cycle number =     19
:
: function value    229.273788    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.140453696    
: Gamma decreased to   0.136948764    
:
:
: fvalues    0.00000000       229.273788       229.253357       229.273788    
:
:
:     CGMAT cycle number =     20
:
: function value    229.253357    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.136948764    
: Gamma decreased to   0.133762464    
:
:
: fvalues    0.00000000       229.253357       229.234314       229.253357    
:
:
:     CGMAT cycle number =      1
:
: function value    3954.63306    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     3.958     3.000
:Bond angles  : others                            26     1.410     3.000
:Torsion angles, period  1. refined               15     1.476    15.000
:Torsion angles, period  1. others                 3     0.190    15.000
:Torsion angles, period  3. refined                4     7.029    15.000
:Chiral centres: refined atoms                     4     0.035     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             1     0.000     0.200
:VDW; torsion: refined_atoms                       6     0.007     0.200
:VDW; torsion.others                               6     0.000     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.00000000    
: Not converging with gamma equal    0.00000000    
: Trying gamma equal    5.50000034E-02
: Gamma decreased to    4.40000035E-02
:
:
: fvalues    0.00000000       3954.63306       1645.58557       3954.63306    
:
:
:     CGMAT cycle number =      2
:
: function value    1645.58557    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.064     0.020
:Bond distances: others                           12     0.011     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    4.40000035E-02
: Gamma decreased to    3.40000018E-02
:
:
: fvalues    0.00000000       1645.58557       1504.83679       1645.58557    
:
:
:     CGMAT cycle number =      3
:
: function value    1504.83679    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.054     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    3.40000018E-02
: Gamma decreased to    2.49090921E-02
:
:
: fvalues    0.00000000       1504.83679       1416.26147       1504.83679    
:
:
:     CGMAT cycle number =      4
:
: function value    1416.26147    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.048     0.020
:Bond distances: others                           12     0.008     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    2.49090921E-02
: Gamma decreased to    1.66446306E-02
:
:
: fvalues    0.00000000       1416.26147       1343.72485       1416.26147    
:
:
:     CGMAT cycle number =      5
:
: function value    1343.72485    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.044     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    1.66446306E-02
: Not converging with gamma equal    1.66446306E-02
: Trying gamma equal    5.79669438E-02
: Gamma decreased to    4.97024804E-02
:
:
: fvalues    0.00000000       1343.72485       1320.16968       1343.72485    
:
:
:     CGMAT cycle number =      6
:
: function value    1320.16968    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    4.97024804E-02
: Not converging with gamma equal    4.97024804E-02
: Trying gamma equal    9.10247937E-02
: Not converging with gamma equal    9.10247937E-02
: Trying gamma equal   0.136479348    
: Gamma decreased to   0.127388433    
:
:
: fvalues    0.00000000       1320.16968       1310.78931       1320.16968    
:
:
:     CGMAT cycle number =      7
:
: function value    1310.78931    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.127388433    
: Gamma decreased to   0.119123973    
:
:
: fvalues    0.00000000       1310.78931       1301.61877       1310.78931    
:
:
:     CGMAT cycle number =      8
:
: function value    1301.61877    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.119123973    
: Gamma decreased to   0.111610822    
:
:
: fvalues    0.00000000       1301.61877       1292.65308       1301.61877    
:
:
:     CGMAT cycle number =      9
:
: function value    1292.65308    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.111610822    
: Gamma decreased to   0.104780689    
:
:
: fvalues    0.00000000       1292.65308       1283.89404       1292.65308    
:
:
:     CGMAT cycle number =     10
:
: function value    1283.89404    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.104780689    
: Gamma decreased to    9.85714793E-02
:
:
: fvalues    0.00000000       1283.89404       1275.34668       1283.89404    
:
:
:     CGMAT cycle number =     11
:
: function value    1275.34668    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    9.85714793E-02
: Gamma decreased to    9.29267406E-02
:
:
: fvalues    0.00000000       1275.34668       1267.01111       1275.34668    
:
:
:     CGMAT cycle number =     12
:
: function value    1267.01111    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    9.29267406E-02
: Not converging with gamma equal    9.29267406E-02
: Trying gamma equal   0.121150434    
: Gamma decreased to   0.115505695    
:
:
: fvalues    0.00000000       1267.01111       1260.57129       1267.01111    
:
:
:     CGMAT cycle number =     13
:
: function value    1260.57129    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.115505695    
: Gamma decreased to   0.110374115    
:
:
: fvalues    0.00000000       1260.57129       1254.25989       1260.57129    
:
:
:     CGMAT cycle number =     14
:
: function value    1254.25989    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.110374115    
: Gamma decreased to   0.105709039    
:
:
: fvalues    0.00000000       1254.25989       1248.08789       1254.25989    
:
:
:     CGMAT cycle number =     15
:
: function value    1248.08789    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.105709039    
: Gamma decreased to   0.101468064    
:
:
: fvalues    0.00000000       1248.08789       1242.05786       1248.08789    
:
:
:     CGMAT cycle number =     16
:
: function value    1242.05786    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.101468064    
: Gamma decreased to    9.76126343E-02
:
:
: fvalues    0.00000000       1242.05786       1236.17566       1242.05786    
:
:
:     CGMAT cycle number =     17
:
: function value    1236.17566    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    9.76126343E-02
: Gamma decreased to    9.41076949E-02
:
:
: fvalues    0.00000000       1236.17566       1230.44861       1236.17566    
:
:
:     CGMAT cycle number =     18
:
: function value    1230.44861    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    9.41076949E-02
: Not converging with gamma equal    9.41076949E-02
: Trying gamma equal   0.111632384    
: Gamma decreased to   0.108127445    
:
:
: fvalues    0.00000000       1230.44861       1225.65967       1230.44861    
:
:
:     CGMAT cycle number =     19
:
: function value    1225.65967    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.108127445    
: Gamma decreased to   0.104941137    
:
:
: fvalues    0.00000000       1225.65967       1220.98193       1225.65967    
:
:
:     CGMAT cycle number =     20
:
: function value    1220.98193    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.104941137    
: Gamma decreased to   0.102044493    
:
:
: fvalues    0.00000000       1220.98193       1216.42285       1220.98193    
:
:
:     CGMAT cycle number =      1
:
: function value    73.1170120    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.038     0.020
:Bond distances: others                           12     0.003     0.020
:Bond angles  : refined atoms                     40     2.254     3.000
:Bond angles  : others                            26     0.421     3.000
:Torsion angles, period  1. refined               15     5.876    15.000
:Torsion angles, period  1. others                 3    15.909    15.000
:Torsion angles, period  3. refined                4    14.029    15.000
:Chiral centres: refined atoms                     4     0.104     0.200
:Planar groups: refined atoms                     14     0.010     0.020
:Planar groups: others                             6     0.001     0.020
:VDW repulsions.others                             4     0.050     0.200
:VDW; torsion: refined_atoms                       4     0.323     0.200
:VDW; torsion.others                               6     0.094     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.00000000    
: Not converging with gamma equal    0.00000000    
: Trying gamma equal    5.50000034E-02
: Gamma decreased to    4.40000035E-02
:
:
: fvalues    0.00000000       73.1170120       28.7609348       73.1170120    
:
:
:     CGMAT cycle number =      2
:
: function value    28.7609348    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.009     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    4.40000035E-02
: Gamma decreased to    3.40000018E-02
:
:
: fvalues    0.00000000       28.7609348       26.8904533       28.7609348    
:
:
:     CGMAT cycle number =      3
:
: function value    26.8904533    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    3.40000018E-02
: Gamma decreased to    2.49090921E-02
:
:
: fvalues    0.00000000       26.8904533       26.4578457       26.8904533    
:
:
:     CGMAT cycle number =      4
:
: function value    26.4578457    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    2.49090921E-02
: Not converging with gamma equal    2.49090921E-02
: Trying gamma equal    7.03636408E-02
: Gamma decreased to    6.12727329E-02
:
:
: fvalues    0.00000000       26.4578457       26.3737450       26.4578457    
:
:
:     CGMAT cycle number =      5
:
: function value    26.3737450    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal    6.12727329E-02
: Not converging with gamma equal    6.12727329E-02
: Trying gamma equal   0.106727280    
: Not converging with gamma equal   0.106727280    
: Trying gamma equal   0.156727284    
: Not converging with gamma equal   0.156727284    
: Trying gamma equal   0.211727291    
: Gamma decreased to   0.200727284    
:
:
: fvalues    0.00000000       26.3737450       26.3533630       26.3737450    
:
:
:     CGMAT cycle number =      6
:
: function value    26.3533630    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.200727284    
: Gamma decreased to   0.190727279    
:
:
: fvalues    0.00000000       26.3533630       26.3372879       26.3533630    
:
:
:     CGMAT cycle number =      7
:
: function value    26.3372879    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.190727279    
: Gamma decreased to   0.181636363    
:
:
: fvalues    0.00000000       26.3372879       26.3240051       26.3372879    
:
:
:     CGMAT cycle number =      8
:
: function value    26.3240051    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.181636363    
: Gamma decreased to   0.173371896    
:
:
: fvalues    0.00000000       26.3240051       26.3128910       26.3240051    
:
:
:     CGMAT cycle number =      9
:
: function value    26.3128910    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.173371896    
: Gamma decreased to   0.165858746    
:
:
: fvalues    0.00000000       26.3128910       26.3033104       26.3128910    
:
:
:     CGMAT cycle number =     10
:
: function value    26.3033104    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.165858746    
: Gamma decreased to   0.159028605    
:
:
: fvalues    0.00000000       26.3033104       26.2950115       26.3033104    
:
:
:     CGMAT cycle number =     11
:
: function value    26.2950115    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.159028605    
: Gamma decreased to   0.152819395    
:
:
: fvalues    0.00000000       26.2950115       26.2877331       26.2950115    
:
:
:     CGMAT cycle number =     12
:
: function value    26.2877331    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.152819395    
: Gamma decreased to   0.147174656    
:
:
: fvalues    0.00000000       26.2877331       26.2812691       26.2877331    
:
:
:     CGMAT cycle number =     13
:
: function value    26.2812691    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.147174656    
: Gamma decreased to   0.142043069    
:
:
: fvalues    0.00000000       26.2812691       26.2754612       26.2812691    
:
:
:     CGMAT cycle number =     14
:
: function value    26.2754612    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.142043069    
: Gamma decreased to   0.137377992    
:
:
: fvalues    0.00000000       26.2754612       26.2702599       26.2754612    
:
:
:     CGMAT cycle number =     15
:
: function value    26.2702599    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.137377992    
: Gamma decreased to   0.133137017    
:
:
: fvalues    0.00000000       26.2702599       26.2656059       26.2702599    
:
:
:     CGMAT cycle number =     16
:
: function value    26.2656059    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.133137017    
: Gamma decreased to   0.129281580    
:
:
: fvalues    0.00000000       26.2656059       26.2613983       26.2656059    
:
:
:     CGMAT cycle number =     17
:
: function value    26.2613983    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.129281580    
: Gamma decreased to   0.125776649    
:
:
: fvalues    0.00000000       26.2613983       26.2576103       26.2613983    
:
:
:     CGMAT cycle number =     18
:
: function value    26.2576103    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.125776649    
: Gamma decreased to   0.122590341    
:
:
: fvalues    0.00000000       26.2576103       26.2542419       26.2576103    
:
:
:     CGMAT cycle number =     19
:
: function value    26.2542419    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.122590341    
: Gamma decreased to   0.119693696    
:
:
: fvalues    0.00000000       26.2542419       26.2511940       26.2542419    
:
:
:     CGMAT cycle number =     20
:
: function value    26.2511940    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.119693696    
: Gamma decreased to   0.117060386    
:
:
: fvalues    0.00000000       26.2511940       26.2484322       26.2511940    
:  Time in seconds: CPU =         0.91
:             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   0.0813  4.066   4.676  1.559   0.043
:       2   0.0      0.0      0.0           0.       0.0   0.0794  3.972   4.318  1.439   0.037
:       3   0.0      0.0      0.0           0.       0.0   0.0760  3.798   4.058  1.353   0.017
:       4   0.0      0.0      0.0           0.       0.0   0.0754  3.772   4.010  1.337   0.026
:       5   0.0      0.0      0.0           0.       0.0   0.0754  3.772   3.985  1.328   0.037
:       6   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.981  1.327   0.036
:       7   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.978  1.326   0.036
:       8   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.969  1.323   0.035
:       9   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.965  1.322   0.035
:      10   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      11   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      12   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      13   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      14   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.962  1.321   0.035
:      15   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      16   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      17   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      18   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      19   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.959  1.320   0.035
:      20   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.958  1.319   0.035
:      21   0.0      0.0      0.0           0.       0.0   0.0637  3.184   2.578  0.859   0.088
:      22   0.0      0.0      0.0           0.       0.0   0.0539  2.697   2.487  0.829   0.085
:      23   0.0      0.0      0.0           0.       0.0   0.0477  2.384   2.425  0.808   0.093
:      24   0.0      0.0      0.0           0.       0.0   0.0436  2.182   2.368  0.789   0.101
:      25   0.0      0.0      0.0           0.       0.0   0.0423  2.114   2.348  0.783   0.105
:      26   0.0      0.0      0.0           0.       0.0   0.0418  2.090   2.340  0.780   0.106
:      27   0.0      0.0      0.0           0.       0.0   0.0414  2.068   2.332  0.777   0.106
:      28   0.0      0.0      0.0           0.       0.0   0.0410  2.049   2.324  0.775   0.106
:      29   0.0      0.0      0.0           0.       0.0   0.0406  2.032   2.316  0.772   0.107
:      30   0.0      0.0      0.0           0.       0.0   0.0403  2.016   2.309  0.770   0.107
:      31   0.0      0.0      0.0           0.       0.0   0.0400  2.002   2.301  0.767   0.107
:      32   0.0      0.0      0.0           0.       0.0   0.0398  1.991   2.295  0.765   0.107
:      33   0.0      0.0      0.0           0.       0.0   0.0396  1.980   2.289  0.763   0.107
:      34   0.0      0.0      0.0           0.       0.0   0.0394  1.970   2.284  0.761   0.106
:      35   0.0      0.0      0.0           0.       0.0   0.0392  1.960   2.278  0.759   0.106
:      36   0.0      0.0      0.0           0.       0.0   0.0390  1.951   2.273  0.758   0.106
:      37   0.0      0.0      0.0           0.       0.0   0.0388  1.942   2.267  0.756   0.105
:      38   0.0      0.0      0.0           0.       0.0   0.0387  1.934   2.263  0.754   0.105
:      39   0.0      0.0      0.0           0.       0.0   0.0385  1.927   2.258  0.753   0.105
:      40   0.0      0.0      0.0           0.       0.0   0.0384  1.919   2.254  0.751   0.104
:      41   0.0      0.0      0.0           0.       0.0   0.0085  0.426   2.770  0.923   0.047
:      42   0.0      0.0      0.0           0.       0.0   0.0069  0.345   2.782  0.927   0.037
:      43   0.0      0.0      0.0           0.       0.0   0.0065  0.326   2.791  0.930   0.035
:      44   0.0      0.0      0.0           0.       0.0   0.0064  0.322   2.794  0.931   0.034
:      45   0.0      0.0      0.0           0.       0.0   0.0064  0.322   2.794  0.931   0.034
:      46   INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 99 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "3GP"
There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/3/3GP.cif
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_11:51:56_2015_modification_0.pdb.gz
There are 2 data in coot-ccp4/libcheck_3GP.cif
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_11:51:56_2015_modification_1.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb
 PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 100 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb
 PDB file /home/paule/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 101 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb
 PDB file /home/paule/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 102 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "LIG"
There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIG.cif
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_11:51:56_2015_modification_2.pdb.gz
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------

(process:14866): GLib-CRITICAL **: Source ID 4294967295 was not found when attempting to remove it
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb
 PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 103 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
 PDB file /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 0/113
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 0/117
  INFO:: fill_ghost_info Constructed 6 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain A"
      Ghost 1 name: "NCS found from matching Chain E onto Chain A"
      Ghost 2 name: "NCS found from matching Chain G onto Chain A"
      Ghost 3 name: "NCS found from matching Chain D onto Chain B"
      Ghost 4 name: "NCS found from matching Chain F onto Chain B"
      Ghost 5 name: "NCS found from matching Chain H onto Chain B"
Molecule 109 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.157 seconds to read MTZ file
INFO:: 0.101 seconds to initialize map
INFO:: 0.089 seconds for FFT
INFO:: 0.013 seconds for statistics
      Map mean: ........ -8.79e-07
      Map sigma: ....... 0.1712
      Map maximum: ..... 1.343
      Map minimum: ..... -0.6954
INFO:: 0.008 seconds for contour map
INFO:: 0.368 seconds in total
INFO:: making difference map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.095 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.076 seconds for FFT
INFO:: 0.013 seconds for statistics
      Map mean: ........ 2.094e-06
      Map sigma: ....... 0.03339
      Map maximum: ..... 0.3661
      Map minimum: ..... -0.1917
INFO:: 0.004 seconds for contour map
INFO:: 0.189 seconds in total
Executing ligand search...
INFO:: ligand number 0 is molecule number 103   with wiggly flag: 0
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    102888
  -0.02498    143000
   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    6
    0.7723    1
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
debug:: n_ligands_for_cluster() top_score 2.007 and 9 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.092 and 4 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.857 and 6 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.387 and 10 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.611 and 8 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.1 and 8 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.691 and 7 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.123 and 2 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.841 and 6 are decent out of 12
Symmetry available for this molecule
INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 123 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_Sun_Sep__6_11:52:09_2015_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_11:52:09_2015_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_11:52:09_2015_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_11:52:09_2015_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/dipole-residues.pdb
 PDB file /home/paule/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 125 read successfully
DEBUG:: there were 0 types with no dictionary 
WARNING: in init_refmac_mon_lib file "/home/paule/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/home/paule/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/home/paule/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
 PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 126 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 126
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 126
INFO:: Reading coordinate file: /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb
 PDB file /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 127 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.032 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.017 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.054e-09
      Map sigma: ....... 0.3115
      Map maximum: ..... 2.978
      Map minimum: ..... -0.875
INFO:: 0.018 seconds for contour map
INFO:: 0.07 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 127

Sequence: ?EYTVITPGARTR
Confidence: 1

From    : HEYTVITPGARTR
Chain id: 0	Offset: 53
INFO:: backup file coot-backup/_home_paule_data_greg-data_crashes_on_cootaneering-v2.pdb_Sun_Sep__6_11:52:12_2015_modification_0.pdb.gz
bypassing ? at 0
Mutating to GLU at 1
Mutating poly_ala residue number 58
Mutating to TYR at 2
Mutating poly_ala residue number 59
Mutating to THR at 3
Mutating poly_ala residue number 60
Mutating to VAL at 4
Mutating poly_ala residue number 61
Mutating to ILE at 5
Mutating poly_ala residue number 62
Mutating to THR at 6
Mutating poly_ala residue number 63
Mutating to PRO at 7
Mutating poly_ala residue number 64
Mutating to GLY at 8
Mutating poly_ala residue number 65
Mutating to ALA at 9
Mutating poly_ala residue number 66
Mutating to ARG at 10
Mutating poly_ala residue number 67
Mutating to THR at 11
Mutating poly_ala residue number 68
Mutating to ARG at 12
Mutating poly_ala residue number 69
DEBUG:: Creating a new chain B
WARNING:: no rotamers probabilities for residue type GLY
INFO:: replace_coords: 9 atoms updated.
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
INFO:: replace_coords: 12 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 8 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
WARNING:: no rotamers probabilities for residue type GLY
WARNING:: no rotamers probabilities for residue type ALA
INFO:: replace_coords: 11 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 11 atoms updated.
INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.01207
    rms devi: 0.01345
    max devi: 0.02142
    min devi: 0.003856
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.2674
    rms devi: 0.3228
    max devi: 0.4951
    min devi: 0.1123
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.0847
INFO:: 5 matched atoms had: 
   mean devi: 0.2674
    rms devi: 0.3228
    max devi: 0.4952
    min devi: 0.1122
INFO:: 5 matched atoms had: 
   mean devi: 0.01198
    rms devi: 0.01335
    max devi: 0.02126
    min devi: 0.003873
INFO:: 5 matched atoms had: 
   mean devi: 0.0002426
    rms devi: 0.0002428
    max devi: 0.0002567
    min devi: 0.0002313
INFO:: 5 matched atoms had: 
   mean devi: 0.2702
    rms devi: 0.335
    max devi: 0.536
    min devi: 0.08456
INFO:: 5 matched atoms had: 
   mean devi: 0.2673
    rms devi: 0.3228
    max devi: 0.4951
    min devi: 0.1124
INFO:: 5 matched atoms had: 
   mean devi: 6.931e-05
    rms devi: 6.936e-05
    max devi: 7.334e-05
    min devi: 6.608e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.01203
    rms devi: 0.01341
    max devi: 0.02135
    min devi: 0.003862
INFO:: 5 matched atoms had: 
   mean devi: 0.0001386
    rms devi: 0.0001387
    max devi: 0.0001467
    min devi: 0.0001322
INFO:: 5 matched atoms had: 
   mean devi: 0.012
    rms devi: 0.01337
    max devi: 0.02129
    min devi: 0.003869
INFO:: 5 matched atoms had: 
   mean devi: 0.2674
    rms devi: 0.3228
    max devi: 0.4952
    min devi: 0.1122
INFO:: 5 matched atoms had: 
   mean devi: 0.2703
    rms devi: 0.3351
    max devi: 0.5361
    min devi: 0.08481
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Sun_Sep__6_11:52:12_2015_modification_0.pdb.gz
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: Matching/moving molecule number 131 to 131
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_Sun_Sep__6_11:52:13_2015_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|         1,  0.003218, -0.003497|
| -0.003225,         1, -0.001985|
|  0.003491,  0.001997,         1|
(    -24.05,     -23.7,    -24.44)
No unit cell for this molecule, hence no fractional matrix.
INFO:: Reading coordinate file: /home/paule/data/greg-data/1wly.pdb
 PDB file /home/paule/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 132 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/paule/data/greg-data/1yb5.pdb
 PDB file /home/paule/data/greg-data/1yb5.pdb has been read.
Spacegroup: P 21 21 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 324/324
INFO:: NCS chain comparison 0/324
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 133 read successfully
DEBUG:: there were 2 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "CL"
There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CL.cif
INFO:: using standard CCP4 Refmac dictionary to search for "NAP"
There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAP.cif
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: reference 132 has 750 atoms selected
INFO:: moving    133 has 842 atoms selected
superposing...
number of Ca atoms in selections: 110 (moving) and 100 (reference)
Another Go...

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

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

 Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY
 Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI

INFO:: backup file coot-backup/_home_paule_data_greg-data_1yb5.pdb_Sun_Sep__6_11:52:14_2015_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|   -0.9117,   -0.3803,    0.1557|
|   -0.3625,    0.9227,     0.131|
|   -0.1935,   0.06299,   -0.9791|
(     70.65,     7.793,     21.29)
  Rotation - polar (omega,phi,kappa)  87.1413 101.0220 169.7385
  Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277
  Translation - Angstroms             70.6538 7.7930 21.2852 
INFO: core rmsd achieved: 1.0199 Angstroems
      number of residues in reference structure: 322
      number of residues in moving structure:    324
      number of residues in aligned sections (reference):  100
      number of residues in aligned sections (moving):     110
      number of aligned residues:  95
      number of gaps:              4
      number of misdirections:     0
      number of SSE combinations:  4.0000
      sequence identity:           30.5263%
WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb
0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.795  0.932   0.034
:      47   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.795  0.932   0.034
:      48   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.795  0.932   0.034
:      49   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.795  0.932   0.034
:      50   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.794  0.931   0.034
:      51   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.794  0.931   0.034
:      52   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.794  0.931   0.034
:      53   0.0      0.0      0.0           0.       0.0   0.0064  0.319   2.794  0.931   0.034
:      54   0.0      0.0      0.0           0.       0.0   0.0064  0.319   2.794  0.931   0.034
:      55   0.0      0.0      0.0           0.       0.0   0.0064  0.319   2.794  0.931   0.034
:      56   0.0      0.0      0.0           0.       0.0   0.0064  0.319   2.793  0.931   0.034
:      57   0.0      0.0      0.0           0.       0.0   0.0064  0.319   2.793  0.931   0.034
:      58   0.0      0.0      0.0           0.       0.0   0.0064  0.319   2.793  0.931   0.034
:      59   0.0      0.0      0.0           0.       0.0   0.0064  0.319   2.793  0.931   0.034
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:
: Refmac_5.7.0029:  End of Refmac_5.7.0029 
:Times: User:       2.9s System:    0.6s Elapsed:     0:04  
:
: : INFO:: libcheck-minimal? is #f PASS: Get monomer test Entered testcase - Set Bond thickness PASS: Set Bond thickness Entered testcase - Delete all-molecule Hydrogens here 1 PASS: Delete all-molecule Hydrogens Entered testcase - Non-Autoloads PASS: Non-Autoloads Entered testcase - Move and Refine Ligand test PASS: Move and Refine Ligand test Entered testcase - Many Molecules - Ligand Fitting Fitting NPO gave these results: # PASS: Many Molecules - Ligand Fitting Entered testcase - flip residue (around eigen vectors) distance: 4.3289603469348 distance d2: 1.33280037492501e-7 PASS: flip residue (around eigen vectors) Entered testcase - Test dipole info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0) PASS: Test dipole Entered testcase - Reading new dictionary restraints replaces PASS: Reading new dictionary restraints replaces Ended 03-ligand.scm Running 04-cootaneer.scm ... Entered testcase - Assignment of new PIR sequence overwrites old assignment debug seq: ("A" . "ACDEFGHIKLMNPQ") PASS: Assignment of new PIR sequence overwrites old assignment Entered testcase - Cootaneer Beta Strand Cootaneering: imol 127 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" PASS: Cootaneer Beta Strand Ended 04-cootaneer.scm Running 05-rna-ghosts.scm ... Entered testcase - RNA NCS Ghosts There are 8 residues in chain "A" There are 8 residues in chain "B" PASS: RNA NCS Ghosts Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example PASS: SSM - Frank von Delft's Example Entered testcase - SSM - Alice Dawson's Example 0 "/home/paule/data/greg-data/tutorial-modern.pdb" 2 "/home/paule/data/greg-data/ins-code-fragment-pre.pdb" 3 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 4 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 5 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 6 "test-3hfl.map" 7 "/home/paule/data/greg-data/tutorial-modern.pdb" 8 "mainchain" 9 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 10 "atom selection from tutorial-add-terminal-1-test.pdb" 11 "/home/paule/data/greg-data/frag-2wot.pdb" 12 "sphere selection from tutorial-modern.pdb" 14 "/home/paule/data/greg-data/rotamer-test-fragment.pdb" 15 "/home/paule/data/greg-data/res098.pdb" 16 "/home/paule/data/greg-data/tutorial-modern.pdb" 17 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 18 "/home/paule/data/greg-data/pdb3knw.ent" 19 "/home/paule/data/greg-data/pdb1py3.ent" 22 "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb" 23 "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 24 "/home/paule/data/greg-data/tutorial-modern.pdb" 25 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 26 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb" 27 "/home/paule/data/greg-data/tutorial-modern.pdb" 28 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 29 "/home/paule/data/greg-data/alt-conf-waters.pdb" 30 "/home/paule/data/greg-data/backrub-fragment.pdb" 31 "Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb" 32 "/home/paule/data/greg-data/coords-B3A.pdb" 33 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" 34 "/home/paule/data/greg-data/test-TER-OXT.pdb" 35 "/home/paule/data/greg-data/val.pdb" 36 "/home/paule/data/greg-data/2yie-frag.pdb" 37 "/home/paule/data/greg-data/4f8g.pdb" 38 "/home/paule/data/greg-data/4f8g.pdb" 39 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 40 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 41 "/home/paule/data/greg-data/tutorial-modern.pdb" 42 "Generic Masked Map" 43 "difference-map" 44 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 45 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 46 "averaged-map" 47 "difference-map" 48 "/home/paule/data/greg-data/multi-carbo-coot-2.pdb" 49 "/home/paule/data/greg-data/monomer-VAL.pdb" 50 "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 51 "atom selection from tutorial-modern.pdb" 52 "/home/paule/data/greg-data/monomer-ACT.pdb" 53 "/home/paule/data/greg-data/tutorial-modern.pdb" 54 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 55 "atom selection from tutorial-modern.pdb" 56 "/home/paule/data/greg-data/tutorial-modern.pdb" 57 "/home/paule/data/greg-data/tutorial-modern.pdb" 58 "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb" 59 "/home/paule/data/greg-data/tutorial-modern.pdb" 60 "/home/paule/data/greg-data/tutorial-modern.pdb" 61 "/home/paule/data/greg-data/pdb3hfl.ent" 62 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 63 "Ideal-A-form-RNA" 64 "Ideal-A-form-RNA" 65 "Ideal-A-form-DNA" 66 "Ideal-A-form-DNA" 67 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 68 "/home/paule/data/greg-data/some-waters-with-ter.pdb" 69 "/home/paule/data/greg-data/tm+some-waters.pdb" 70 "/home/paule/data/greg-data/tutorial-modern.pdb" 71 "/home/paule/data/greg-data/water-test-no-cell.pdb" 72 "/home/paule/data/greg-data/pathological-water-test.pdb" 73 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 74 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 75 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 76 "/home/paule/data/greg-data/tutorial-modern.pdb" 77 "/home/paule/data/greg-data/pdb1hvv.ent" 78 "/home/paule/data/greg-data/monomer-ACT.pdb" 79 "/home/paule/data/greg-data/monomer-NPO.pdb" 80 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_77" 81 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 82 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb" 83 "/home/paule/data/greg-data/tutorial-modern.pdb" 84 "/home/paule/data/greg-data/pdb1py3.ent" 85 "/home/paule/data/greg-data/tutorial-modern.pdb" 86 "/home/paule/data/greg-data/tutorial-modern.pdb" 87 "/home/paule/data/greg-data/2goz-manip.pdb" 88 "/home/paule/data/greg-data/HOF.RES" 89 "/home/paule/INFO:: Reading coordinate file: /home/paule/data/greg-data/2qd9.pdb PDB file /home/paule/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 134 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LGF" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LGF.cif INFO:: Reading coordinate file: /home/paule/data/greg-data/2gtn.pdb PDB file /home/paule/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 0/337 Molecule 135 read successfully DEBUG:: there were 1 types with no dictionary INFO:: using standard CCP4 Refmac dictionary to search for "LIE" There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIE.cif INFO:: reference 134 has 169 atoms selected INFO:: moving 135 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance(/A) A 140 <---> A 140 : 0.1804 A 141 <---> A 141 : 0.0760 A 142 <---> A 142 : 0.1052 A 143 <---> A 143 : 0.1246 A 144 <---> A 144 : 0.1370 A 145 <---> A 145 : 0.1380 A 146 <---> A 146 : 0.1662 A 147 <---> A 147 : 0.2744 A 148 <---> A 148 : 0.2728 A 149 <---> A 149 : 0.1173 A 150 <---> A 150 : 0.1684 A 151 <---> A 151 : 0.0928 A 152 <---> A 152 : 0.1200 A 153 <---> A 153 : 0.1281 A 154 <---> A 154 : 0.2539 A 155 <---> A 155 : 0.6351 A 156 <---> A 156 : 0.1300 A 157 <---> A 157 : 0.1478 A 158 <---> A 158 : 0.2238 A 159 <---> A 159 : 0.2271 A 160 <---> A 160 : 0.2372 Moving: YIHSADIIHRDLKPSNLAVNE Target: YIHSADIIHRDLKPSNLAVNE INFO:: backup file coot-backup/_home_paule_data_greg-data_2gtn.pdb_Sun_Sep__6_11:52:15_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491 Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832 Translation - Angstroms 0.3207 0.6598 0.8819 INFO: core rmsd achieved: 0.2210 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1.0000 sequence identity: 100.0000% LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000 READ-INS:: Spacegroup: "I 21 3" INFO:: chain has 121 residues Symmetry available for this molecule Molecule 136 read successfully INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.0310 seconds to read MTZ file INFO:: 0.0000 seconds to initialize map INFO:: 0.0170 seconds for FFT INFO:: 0.0020 seconds for statistics Map mean: ........ 0.0000 Map sigma: ....... 0.3115 Map maximum: ..... 2.9776 Map minimum: ..... -0.8750 INFO:: 0.0170 seconds for contour map INFO:: 0.0670 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:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0004 st.d: 0.3236 Map statistics: min: -1.4496, max: 2.3411 -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 1 2.3885 1 INFO:: installing ghost map with name :Map 137 NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2.0000 maps contributing to the average INFO:: rescaling by 0.5000 INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.0004 st.d: 0.3236 Map statistics: min: -1.4496, max: 2.3411 -1.4022 3 -1.3074 1 -1.2127 4 -1.1179 8 -1.0231 5 -0.9283 32 -0.8336 104 -0.7388 349 -0.6440 1163 -0.5493 3433 -0.4545 8783 -0.3597 17620 -0.2650 27133 -0.1702 32345 -0.0754 31462 0.0193 26827 0.1141 20587 0.2089 15419 0.3036 11965 0.3984 8787 0.4932 6637 0.5879 4777 0.6827 3343 0.7775 2426 0.8722 1733 0.9670 1142 1.0618 796 1.1565 469 1.2513 296 1.3461 188 1.4409 96 1.5356 80 1.6304 34 1.7252 20 1.8199 14 1.9147 6 2.0095 4 2.1042 3 2.1990 0 2.2938 1 2.3885 1 no diffs NCS target chain has 93 peers. INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 142 read successfully DEBUG:: there were 0 types with no dictionary INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:52:17_2015_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:52:17_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:52:17_2015_modification_2.pdb.gz %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 142 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 142 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.3643 rms devi: 0.4571 max devi: 2.1351 min devi: 0.0881 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:52:17_2015_modification_3.pdb.gz INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:52:17_2015_modification_4.pdb.gz DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 142 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 142 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 92/93 First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700 First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 0.3427 rms devi: 0.4454 max devi: 2.1352 min devi: 0.0124 find_ncs_matrix returns (LSQ) | 0.9705, -0.04643, -0.2365| | 0.2356, 0.3891, 0.8906| | 0.05068, -0.92, 0.3886| ( 37.8, -17.17, 13.81) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: set_ncs_master_chain Constructed 1 ghosts Ghost info:: NCS found from matching Chain B onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_11:52:17_2015_modification_5.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1t6q.ent PDB file /home/paule/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 143 read successfully DEBUG:: there were 0 types with no dictionary INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Sun_Sep__6_11:52:18_2015_modification_0.pdb.gz %%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 143 and ichain: 0 DEBUG:: ncs_control_change_ncs_master_to_chain imol: 143 and ichain: 0 %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 0 Checking chains for NCS matching to chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2048 rms devi: 0.2651 max devi: 1.1707 min devi: 0.0160 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) Adding ghost with name: NCS found from matching Chain B onto Chain A INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800 First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.2275 rms devi: 0.3035 max devi: 1.6549 min devi: 0.0661 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) Adding ghost with name: NCS found from matching Chain C onto Chain A INFO:: set_ncs_master_chain Constructed 2 ghosts Ghost info:: NCS found from matching Chain B onto Chain A Ghost info:: NCS found from matching Chain C onto Chain A INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Sun_Sep__6_11:52:18_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Sun_Sep__6_11:52:18_2015_modification_2.pdb.gz INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 144 read successfully DEBUG:: there were 0 types with no dictionary DEBUG ncs_control_change_ncs_master_to_chain_id imol: 144 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 145 to 144 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.2239 rms devi: 0.2350 max devi: 0.3369 min devi: 0.0588 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Sun_Sep__6_11:52:19_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) Symmetry available for this molecule INFO:: Matching/moving molecule number 146 to 144 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.1943 rms devi: 0.2112 max devi: 0.3583 min devi: 0.0329 INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095) INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Sun_Sep__6_11:52:19_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.6203, -0.2279, -0.7505| | -0.4559, -0.6739, 0.5814| | -0.6382, 0.7028, 0.3141| ( -22.14, -19.93, 1.626) INFO:: fractional coordinates matrix: | -0.8835, -0.09252, -0.543| | -0.5264, -0.4107, 0.8789| | -0.4875, 0.7087, 0.3141| ( -0.381, -0.2605, 0.01406) Symmetry available for this molecule INFO:: Matching/moving molecule number 147 to 144 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.4174 rms devi: 0.4531 max devi: 0.7926 min devi: 0.0759 INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411) INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Sun_Sep__6_11:52:20_2015_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 148 read successfully DEBUG:: there were 0 types with no dictionary INFO:: making map from mtz filename /home/paule/data/greg-data/1hvv_sigmaa.mtz Number of OBSERVED reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5000 INFO grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.0420 seconds to read MTZ file INFO:: 0.0220 seconds to initialize map INFO:: 0.0310 seconds for FFT INFO:: 0.0030 seconds for statistics Map mean: ........ -0.0000 Map sigma: ....... 0.2241 Map maximum: ..... 1.7219 Map minimum: ..... -0.8818 INFO:: 0.0090 seconds for contour map INFO:: 0.1070 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 149 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 149 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 149 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5946 0.3997 3628 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 149 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 149 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 149 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5946 0.3997 3628 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 INFO:: installing ghost map with name :Map 149 NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 149 NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :Map 149 NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4.0000 maps contributing to the average INFO:: rescaling by 0.2500 INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.0008 st.d: 0.1767 Map statistics: min: -0.9977, max: 1.4866 -0.9667 1 -0.9046 3 -0.8424 8 -0.7803 10 -0.7182 37 -0.6561 102 -0.5940 196 -0.5319 490 -0.4698 1190 -0.4077 2390 -0.3456 4703 -0.2835 8981 -0.2214 16028 -0.1593 27796 -0.0972 44285 -0.0351 60780 0.0271 53651 0.0892 32327 0.1513 21048 0.2134 14284 0.2755 9269 0.3376 5946 0.3997 3628 0.4618 2439 0.5239 1480 0.5860 942 0.6481 569 0.7102 378 0.7723 239 0.8344 166 0.8965 112 0.9587 94 1.0208 50 1.0829 35 1.1450 21 1.2071 17 1.2692 5 1.3313 4 1.3934 5 1.4555 3 1.5176 0 error (syntax error) error (syntax error) error (not syntax error) Traceback (most recent call last): File "", line 1, in NameError: name 'rr_not_found_thing' is not defined INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 158 read successfully DEBUG:: there were 0 types with no dictionary Entering test: OXT in restraints? INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/paule/data/greg-data/libcheck_BCS.cif PASS: OXT in restraints? Entering test: Relative file name PASS: Relative file name Entering test: geometry distortion comparision Good gdi < exception thrown Good gdi > exception thrown PASS: geometry distortion comparision Entering test: test symm trans to origin Got length 0.1414 PASS: test symm trans to origin Entering test: test lsq plane LSQ deviations: 0.0000 0.0000 PASS: test lsq plane Entering test: test COO modification INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ There are 125 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif There are 2 data in /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif INFO:: Reading coordinate file: /home/paule/data/greg-data/hideous-OXT.pdb PDB file /home/paule/data/greg-data/hideous-OXT.pdb has been read. Spacegroup: P 21 21 21 read 9 atom created 7 bond restraints created 8 angle restraints created 1 plane restraints created 1 chiral vol restraints created 2 torsion restraints created 23 restraints INFO:: make_restraints(): made 20 non-bonded restraints initial distortion_score: 5677.4757 Initial RMS Z values bonds: 3.7208 angles: 7.4688 torsions: 0.2764 planes: 16.9011 non-bonded: 221.7967 chiral vol: 1.2266 rama plot: N/A start_pos: N/A GemanMcCl: N/A Minimum found (iteration number 895) at 21.2864 Final Estimated RMS Z Scores: bonds: 1.0044 angles: 0.8989 torsions: 0.0371 planes: 0.0012 non-bonded: 0.2566 chiral vol: 0.0046 rama plot: N/A start_pos: N/A GemanMcCl: N/A refinement_took 0.0190 seconds OXT out of plane distance: 0.0001 OXT->O distance: 2.2547 PASS: test COO modification Entering test: remove whitespace PASS: remove whitespace Entering test: New comp_ids are sane PASS: New comp_ids are sane Entering test: Residues for phi,psi are close enough to be considered linked INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read. Spacegroup: P 21 21 21 bad residues for phi,psi calculation bad residues for phi,psi calculation PASS: Residues for phi,psi are close enough to be considered linked data/greg-data/hollander.ins" 92 "/home/paule/data/greg-data/insulin.fcf" 93 "atom selection from insulin.res" 94 "atom selection from insulin.res" 96 "/home/paule/data/greg-data/horma-p21.res" 97 "new-horma.ins" 98 "/home/paule/data/greg-data/crash.hat" 99 "coot-ccp4/monomer-3GP.pdb" 100 "/home/paule/data/greg-data/monomer-3GP.pdb" 101 "/home/paule/data/greg-data/test-LIG.pdb" 102 "/home/paule/data/greg-data/test-LIG.pdb" 103 "/home/paule/data/greg-data/monomer-NPO.pdb" 104 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 105 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 106 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 107 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 108 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb" 109 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 110 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 111 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 112 "Masked (by protein)" 113 "Fitted ligand #0-0" 114 "Fitted ligand #1-0" 115 "Fitted ligand #2-0" 116 "Fitted ligand #3-0" 117 "Fitted ligand #4-0" 118 "Fitted ligand #5-0" 119 "Fitted ligand #6-0" 120 "Fitted ligand #7-0" 121 "Fitted ligand #8-0" 122 "Fitted ligand #9-0" 123 "coot-ccp4/monomer-3GP.pdb" 124 "Copy_of_coot-ccp4/monomer-3GP.pdb" 125 "/home/paule/data/greg-data/dipole-residues.pdb" 126 "/home/paule/data/greg-data/tutorial-modern.pdb" 127 "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb" 128 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 129 "Ideal-A-form-RNA" 132 "/home/paule/data/greg-data/1wly.pdb" 133 "/home/paule/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 149 NCS found from matching Chain B onto Chain A" n-matchers: 2 ==== test-name: "Map 149 NCS found from matching Chain C onto Chain A" n-matchers: 2 ==== test-name: "Map 149 NCS found from matching Chain D onto Chain A" n-matchers: 2 PASS: NCS maps overwrite existing maps Ended 07-ncs.scm Running 08-utils.scm ... Entered testcase - Test key symbols WARNING:: could not find key-sym-code for "missing key" PASS: Test key symbols Entered testcase - Test running a Python function test_val_2 passed test_val_3 passed PASS: Test running a Python function Entered testcase - Internal/External Molecule Numbers match PASS: Internal/External Molecule Numbers match Entered testcase - spacegroup operators to space group conversion PASS: spacegroup operators to space group conversion Ended 08-utils.scm Running 09-internal.scm ... Entered testcase - Test internal functions PASS: Test internal functions Ended 09-internal.scm === greg-tests Summary === # of testcases attempted 117 # of expected passes 117 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 Loading greg-tests/end.grg ... Loaded greg-tests/end.grg === Summary of all tests === # of tools 1 # of testcases attempted 117 # of expected passes 117 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 0 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 test_coot: coot test passed