testing with greg
testing with greg
currently we are here:
/lmb/home/pemsley/autobuild/building/lg19.lmb.internal_2015-09-06__T05_00_08/coot-0.8.3-pre
Sun Sep 6 06:05:33 BST 2015
WARNING:: ccp4 setup file setup-ccp4 does not exist.
/lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/
There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/AR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CD.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GD.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif
INFO:: Reading coordinate file: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/standard-residues.pdb
PDB file /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
initalize graphics molecules...done.
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
[1m(use-graphics-interface-state)[0m
Importing python module coot using command from coot import *
INFO:: coot.py imported
Running python script /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-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
[1m(set-display-intro-string "Good Morning None, Welcome to Coot. 0.8.3-pre")[0m
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
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
[1m(use-graphics-interface-state)[0m
Loading scheme files from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/scheme
[1m(set-display-intro-string "Good morning Paul. Welcome to Coot")[0m
[1m(set-display-lists-for-maps 0)[0m
INFO:: loading preferences file /lmb/home/pemsley/.coot-preferences/angle-factor.scm
[1m(set-hardware-stereo-angle-factor 1.50)[0m
INFO:: loading preferences file /lmb/home/pemsley/.coot-preferences/coot-preferences.scm
[1m(set-filter-fileselection-filenames 1)[0m
[1m(set-sticky-sort-by-date)[0m
[1m(set-colour-map-rotation-on-read-pdb 21.00)[0m
[1m(set-colour-map-rotation-on-read-pdb-c-only-flag 1)[0m
[1m(set-density-size 12.60)[0m
[1m(set-swap-difference-map-colours 0)[0m
[1m(set-colour-map-rotation-for-map 14.00)[0m
[1m(set-active-map-drag-flag 1)[0m
[1m(set-idle-function-rotate-angle 0.10)[0m
INFO:: loading preferences file /lmb/home/pemsley/.coot-preferences/enhanced-ligand.scm
INFO:: loading preferences file /lmb/home/pemsley/.coot-preferences/key-bindings.scm
[1m(set-add-terminal-residue-do-post-refine 1)[0m
[1m(set-terminal-residue-do-rigid-body-refine 0)[0m
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
Loading ~/.coot...done.
INFO:: There are 1 command line scripts to run
command-line-greg.scm
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 0 read successfully
DEBUG:: there were 0 types with no dictionary
Molecule number -5 is not a valid model molecule
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2WF6.cif
mmCIF file /lmb/home/pemsley/data/greg-data/2WF6.cif has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 1 read successfully
DEBUG:: there were 3 types with no dictionary
INFO:: using standard CCP4 Refmac dictionary to search for "ALF"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALF.cif
INFO:: using standard CCP4 Refmac dictionary to search for "MG"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MG.cif
INFO:: using standard CCP4 Refmac dictionary to search for "BG6"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/b/BG6.cif
in new_molecule_by_atom_selection Something bad happened - No atoms selected
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb
PDB file /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 2 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Creating directory coot-backup
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Sun_Sep__6_06:05:35_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Sun_Sep__6_06:05:35_2015_modification_1.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Sun_Sep__6_06:05:35_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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.037 seconds to read MTZ file
INFO:: 0.012 seconds to initialize map
INFO:: 0.016 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.06932e-09
Map sigma: ....... 0.311501
Map maximum: ..... 2.97757
Map minimum: ..... -0.875045
INFO:: 0.02 seconds for contour map
INFO:: 0.088 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: /lmb/home/pemsley/data/greg-data/broken.mtz
INFO:: not an mtz file: /lmb/home/pemsley/data/greg-data/broken.mtz
INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 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: ........ 1.06932e-09
Map sigma: ....... 0.311501
Map maximum: ..... 2.97757
Map minimum: ..... -0.875045
INFO:: 0.02 seconds for contour map
INFO:: 0.069 seconds in total
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz
Number of OBSERVED reflections: 17920
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 64, 96, 90)
INFO:: 0.027 seconds to read MTZ file
INFO:: 0.006 seconds to initialize map
INFO:: 0.012 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 2.00384e-11
Map sigma: ....... 0.260405
Map maximum: ..... 1.71787
Map minimum: ..... -1.03389
INFO:: 0.005 seconds for contour map
INFO:: 0.053 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: 2.00384e-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
-0.0363793 43098
0.0324147 41219
0.101209 29087
0.170003 15906
0.238797 8720
0.307591 6095
0.376385 4870
0.445179 4308
0.513973 3717
0.582767 3304
0.651561 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: 2.00384e-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: ........ 4.037e-06
Map rmsd: ........ 0.2604
Map maximum: ..... 1.718
Map minimum: ..... -1.034
WARNING:: Error reading .
. is a directory.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 7 read successfully
DEBUG:: there were 0 types with no dictionary
/lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures successfully opened
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
9 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
174 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
226 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
228 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
72 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
24 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
145 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
29 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
155 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
52 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
349 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
35 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
364 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
13 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
218 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
56 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb
There was an error reading /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb.
ERROR 42 READ: Duplicate sequence number and insertion code.
LINE #868
ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
171 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
129 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
33 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
543 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
23 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
45 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
54 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
294 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
131 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
208 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
119 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
14 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
318 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
172 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
20 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
106 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
123 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
142 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
127 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
51 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
205 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
149 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
140 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
143 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
137 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
520 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
326 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
4 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
411 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
136 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
75 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
247 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
494 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
64 fragments garnered from /lmb/home/pemsley/autobuild/Linux-lg19.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
INFO:: 8375 fragments found in total of which 0 were 5 peptides
target fragment start res: 10 had 29 db fragment hits, ilength=6
target fragment start res: 13 had 1772 db fragment hits, ilength=6
breaking out of match_target_fragment 6 with iresno= 16
merge fragments 10 to 20 with 2 fit sets to merge
The merging is complete
mainchain_fragment from 10 to 20
done mainchain_fragment
successfully set cell and symmetry
Symmetry available for this molecule
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 83/90
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 9 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Masking around 41 atoms
fitting terminal residue with 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/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_06:05:38_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_06:05:38_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/frag-2wot.pdb
PDB file /lmb/home/pemsley/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 11 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_06:05:38_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_06:05:38_2015_modification_1.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_06:05:38_2015_modification_2.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb
PDB file /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 14 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading rotamer probability tables...
primitive chis: Failure to find correct atom quads in residue atoms
quad needed: : N : : CA : : CB : : OG1:
INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""]
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/res098.pdb
PDB file /lmb/home/pemsley/data/greg-data/res098.pdb has been read.
Spacegroup: P 41 21 2
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 15 read successfully
DEBUG:: there were 0 types with no dictionary
created 6 bond restraints
created 6 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 13 restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints:
2 bond links
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): 4.327
debug:: restraints results 1 5
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_res098.pdb_Sun_Sep__6_06:05:39_2015_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 16 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.016 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.023 seconds for contour map
INFO:: 0.07 seconds in total
here in split_residue()
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:39_2015_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0
debug:: split_residue() returned 0 ""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:39_2015_modification_1.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 11.75
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3knw.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb3knw.ent has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 30 links
Symmetry available for this molecule
INFO:: NCS chain comparison 185/199
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 18 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: using standard CCP4 Refmac dictionary to search for "EDO"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/e/EDO.cif
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3knw.ent_Sun_Sep__6_06:05:40_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 91/204
INFO:: NCS chain comparison 90/204
INFO:: NCS chain comparison 175/179
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain C onto Chain B"
Molecule 19 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1py3.ent_Sun_Sep__6_06:05:40_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: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 20 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.016 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.022 seconds for contour map
INFO:: 0.069 seconds in total
here in split_residue()
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:40_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: /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb
PDB file /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 22 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-pepflip-test.pdb_Sun_Sep__6_06:05:40_2015_modification_0.pdb.gz
flipped 65 A
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 23 read successfully
DEBUG:: there were 0 types with no dictionary
in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x4a6e200
omega: 1 12.77 degrees
INFO This is a CIS peptide - making it TRANS
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_06:05:40_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_06:05:40_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/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_06:05:40_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 3) 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: 0.06899
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 5.689
Refinement elapsed time: 0.015
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_06:05:40_2015_modification_3.pdb.gz
INFO:: replace_coords: 11 atoms updated.
INFO:: mutate 11 A to a LEU
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_06:05:40_2015_modification_4.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_06:05:40_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: 4.829
non-bonded: 1.367
chiral vol: 0.5215
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 46) at -5912
Final Estimated RMS Z Scores:
bonds: 1.796
angles: 1.21
torsions: N/A
planes: 3.485
non-bonded: 0.6665
chiral vol: 0.1097
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 5.822
Refinement elapsed time: 0.014
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Sun_Sep__6_06:05:40_2015_modification_6.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 24 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.015 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.022 seconds for contour map
INFO:: 0.07 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 26) at -2868
Final Estimated RMS Z Scores:
bonds: 1.366
angles: 1.425
torsions: N/A
planes: 2.035
non-bonded: 4.218
chiral vol: 0.6015
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 6.08
Refinement elapsed time: 0.006
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:41_2015_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 83/90
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 26 read successfully
DEBUG:: there were 0 types with no dictionary
here in split_residue()
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_06:05:41_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 30) 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): 6.401
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_06:05:41_2015_modification_1.pdb.gz
INFO:: replace_coords: 23 atoms updated.
created 36 bond restraints
created 40 angle restraints
created 3 plane restraints
created 5 chiral vol restraints
created 84 restraints
Link restraints:
4 bond links
12 angle links
8 plane links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
0 parallel plane restraints
INFO:: make_restraints(): made 1031 non-bonded restraints
initial distortion_score: -1.249e+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 53) at -1.584e+04
Final Estimated RMS Z Scores:
bonds: 1.681
angles: 1.892
torsions: N/A
planes: 2.024
non-bonded: 0.005873
chiral vol: 1.841
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 6.68
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Sun_Sep__6_06:05:41_2015_modification_2.pdb.gz
INFO:: replace_coords: 41 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 27 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.016 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.021 seconds for contour map
INFO:: 0.069 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 36) 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): 7.023
Refinement elapsed time: 0.091
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: -426.4
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 10) at -2664
Final Estimated RMS Z Scores:
bonds: 0.5489
angles: 1.686
torsions: N/A
planes: 1.369
non-bonded: 0.008326
chiral vol: 1.322
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 7.197
Refinement elapsed time: 0.173
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: 471
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 19) at -1700
Final Estimated RMS Z Scores:
bonds: 0.4278
angles: 1.637
torsions: N/A
planes: 1.17
non-bonded: 0.00641
chiral vol: 1.276
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 7.401
Refinement elapsed time: 0.204
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: 841.6
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 49) at -1308
Final Estimated RMS Z Scores:
bonds: 0.3693
angles: 1.616
torsions: N/A
planes: 1.059
non-bonded: 0.005138
chiral vol: 1.304
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 8.037
Refinement elapsed time: 0.636
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb
PDB file /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 29 read successfully
DEBUG:: there were 0 types with no dictionary
masking....masking done
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-waters.pdb_Sun_Sep__6_06:05:43_2015_modification_0.pdb.gz
INFO:: replace_coords: 1 atoms updated.
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb
PDB file /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 30 read successfully
DEBUG:: there were 0 types with no dictionary
Symmetry available for this molecule
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Sun_Sep__6_06:05:43_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Sun_Sep__6_06:05:43_2015_modification_1.pdb.gz
INFO:: replace_coords: 14 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/coords-B3A.pdb
PDB file /lmb/home/pemsley/data/greg-data/coords-B3A.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 32 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: using standard CCP4 Refmac dictionary to search for "B3A"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/b/B3A.cif
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 11 restraints
INFO:: make_restraints(): made 5 non-bonded restraints
initial distortion_score: 2.951
Initial RMS Z values
bonds: 0.6619
angles: 0.3737
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.25
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 28) at 4.058e-05
Final Estimated RMS Z Scores:
bonds: 0.0005327
angles: 0.002779
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.0007482
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 8.547
debug:: restraints results 1 4
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Sun_Sep__6_06:05:43_2015_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
WARNING: in init_refmac_mon_lib file "/lmb/home/pemsley/data/greg-data/lib-B3A.cif not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/lib-B3A.cif had no bond restraints
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 11 restraints
INFO:: make_restraints(): made 5 non-bonded restraints
initial distortion_score: 4.058e-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): 8.63
debug:: restraints results 1 4
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Sun_Sep__6_06:05:43_2015_modification_1.pdb.gz
INFO:: replace_coords: 6 atoms updated.
There are 3 data in /lmb/home/pemsley/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): 8.724
debug:: restraints results 1 4
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_coords-B3A.pdb_Sun_Sep__6_06:05:43_2015_modification_2.pdb.gz
INFO:: replace_coords: 6 atoms updated.
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.014 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.016 seconds for contour map
INFO:: 0.059 seconds in total
INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb
PDB file /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 34 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_test-TER-OXT.pdb_Sun_Sep__6_06:05:44_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: /lmb/home/pemsley/data/greg-data/val.pdb
PDB file /lmb/home/pemsley/data/greg-data/val.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 35 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: mutate 3 C to a HIS
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_val.pdb_Sun_Sep__6_06:05:44_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2yie-frag.pdb
PDB file /lmb/home/pemsley/data/greg-data/2yie-frag.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 36 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2yie-frag.pdb_Sun_Sep__6_06:05:44_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: /lmb/home/pemsley/data/greg-data/4f8g.pdb
PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 37 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: using standard CCP4 Refmac dictionary to search for "NCO"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NCO.cif
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Sun_Sep__6_06:05:44_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: /lmb/home/pemsley/data/greg-data/4f8g.pdb
PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 38 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Sun_Sep__6_06:05:44_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 /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.024 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.014 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.015 seconds for contour map
INFO:: 0.056 seconds in total
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.2
INFO grid sampling...Nuvw = ( 160, 192, 96)
INFO:: 0.027 seconds to read MTZ file
INFO:: 0.031 seconds to initialize map
INFO:: 0.028 seconds for FFT
INFO:: 0.007 seconds for statistics
Map mean: ........ 1.229e-09
Map sigma: ....... 0.3115
Map maximum: ..... 3.052
Map minimum: ..... -0.9217
INFO:: 0.036 seconds for contour map
INFO:: 0.129 seconds in total
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 41 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Masking around 64 atoms
Map statistics: mean: -0.001403 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
load "filter.scm"
load "matrices.scm"
load "coot-utils.scm"
load "redefine-functions.scm"
load "json-reader.scm"
load "coot-lsq.scm"
load "shelx.scm"
load "get-ebi.scm"
load "local-code.scm"
load "hello.scm"
Good morning Paul Emsley PI Garib Murshudov added 28092012. 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
Entered testcase - Hs are correctly swapped on a TYR
results: (#t #t #t #t)
PASS: Hs are correctly swapped on a TYR
Entered testcase - Splitting residue leaves no atoms with negative occupancy
PASS: Splitting residue leaves no atoms with negative occupancy
Entered testcase - Pepflip flips the correct alt confed atoms
PASS: Pepflip flips the correct alt confed atoms
Entered testcase - Correction of CISPEP test
CISPEPs: "3"
PASS: Correction of CISPEP test
Entered testcase - Refine Zone with Alt conf
refined moved: d=0.301590070988641
PASS: Refine Zone with Alt conf
Entered testcase - Sphere Refine
======= got bond length 1.29337078990428
PASS: Sphere Refine
Entered testcase - Refinement gives useful results
refinement results: ("" 0 (("Bonds" "Bonds: 1.770" 1.77020490169525) ("Angles" "Angles: 2.093" 2.0928328037262) ("Planes" "Planes: 2.225" 2.22536563873291) ("Non-bonded" "Non-bonded: 0.137" 0.136829659342766) ("Chirals" "Chirals: 1.990" 1.98977398872375)))
ow factor: 2.01954433321953
INFO:: setting refinement weight to 14.711076971815
refinement results: ("" 0 (("Bonds" "Bonds: 0.549" 0.548932790756226) ("Angles" "Angles: 1.686" 1.68627393245697) ("Planes" "Planes: 1.369" 1.36898624897003) ("Non-bonded" "Non-bonded: 0.091" 0.0912495031952858) ("Chirals" "Chirals: 1.322" 1.3219997882843)))
ow factor: 1.23154819011688
INFO:: setting refinement weight to 9.69932787062618
refinement results: ("" 0 (("Bonds" "Bonds: 0.428" 0.427833706140518) ("Angles" "Angles: 1.637" 1.63650107383728) ("Planes" "Planes: 1.170" 1.16983282566071) ("Non-bonded" "Non-bonded: 0.080" 0.0800608173012733) ("Chirals" "Chirals: 1.276" 1.27578890323639)))
ow factor: 1.12748912721872
INFO:: setting refinement weight to 7.62986576305762
refinement results: ("" 0 (("Bonds" "Bonds: 0.369" 0.369307339191437) ("Angles" "Angles: 1.616" 1.61550199985504) ("Planes" "Planes: 1.059" 1.05890274047852) ("Non-bonded" "Non-bonded: 0.072" 0.0716812461614609) ("Chirals" "Chirals: 1.304" 1.30414485931396)))
ow factor: 1.08696423470974
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 0.963148653507233 0.588746011257172 0.692066609859467 0.75197696685791 0.68085777759552 0.954908967018127 1.00084149837494 0.981854557991028 0.726146459579468) 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 3
0.7744 1
diff-high-values: (0.00255927024409175 0.00100332591682673 0.00106663466431201 -0.00237777037546039 0.00169648602604866 7.11897853761911e-4 0.00212944112718105 0.00194918387569487 0.00229502376168966 6.55884097795933e-4 0.00835355557501316) diff-low-values: (-0.887997210025787 -0.79390150308609 -1.18933153152466 -1.06666219234467 -0.988452911376953 -0.759092569351196 -0.748683869838715 -0.650666236877441 -0.90451979637146 -0.545242011547089)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.024 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.014 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.015 seconds for contour map
INFO:: 0.055 seconds in total
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.5
INFO grid sampling...Nuvw = ( 180, 216, 108)
INFO:: 0.025 seconds to read MTZ file
INFO:: 0.045 seconds to initialize map
INFO:: 0.037 seconds for FFT
INFO:: 0.009 seconds for statistics
Map mean: ........ 1.161e-09
Map sigma: ....... 0.3115
Map maximum: ..... 3.071
Map minimum: ..... -0.8775
INFO:: 0.049 seconds for contour map
INFO:: 0.165 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
-0.004743 114
-0.004274 221
-0.003804 460
-0.003335 817
-0.002865 1522
-0.002396 2765
-0.001926 4797
-0.001457 9241
-0.0009873 19276
-0.0005178 40375
-4.828e-05 61227
0.0004212 44297
0.0008908 20927
0.00136 9474
0.00183 4784
0.002299 2778
0.002769 1680
0.003238 1171
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: /lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb
PDB file /lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/f/FUC.cif
INFO:: using standard CCP4 Refmac dictionary to search for "NAG"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NAG.cif
created 46 bond restraints
created 82 angle restraints
created 2 plane restraints
created 8 chiral vol restraints
created 138 restraints
INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A
INFO:: glycosidic_linkage type :ALPHA1-4:
Link restraints:
1 bond links
3 angle links
0 plane links
0 parallel plane restraints
INFO:: make_restraints(): made 671 non-bonded restraints
initial distortion_score: 7037
Initial RMS Z values
bonds: 11.36
angles: 3.259
torsions: N/A
planes: 0.08353
non-bonded: 0.09438
chiral vol: 0.9035
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 397) at 0.7474
Final Estimated RMS Z Scores:
bonds: 0.02236
angles: 0.09026
torsions: N/A
planes: 0.001388
non-bonded: 2.091e-05
chiral vol: 0.04659
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 10.98
debug:: restraints results 1 5
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_multi-carbo-coot-2.pdb_Sun_Sep__6_06:05:46_2015_modification_0.pdb.gz
INFO:: replace_coords: 46 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb
PDB file /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 49 read successfully
DEBUG:: there were 0 types with no dictionary
created 14 bond restraints
created 25 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 40 restraints
INFO:: make_restraints(): made 44 non-bonded restraints
initial distortion_score: 4.997
Initial RMS Z values
bonds: 0.5425
angles: 0.1641
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.4516
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 80) at 0.2476
Final Estimated RMS Z Scores:
bonds: 0.01102
angles: 0.09486
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.1448
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 11.29
debug:: restraints results 1 4
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_06:05:46_2015_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: undo molecule number set to: 49
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_06:05:46_2015_modification_1.pdb.gz
restoring from backup 2 2
INFO:: Reading coordinate file: coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_06:05:46_2015_modification_0.pdb.gz
PDB file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_06:05:46_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): 11.37
debug:: restraints results 1 4
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Sun_Sep__6_06:05:46_2015_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb
PDB file /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 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): 11.76
debug:: restraints results 1 4
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Sun_Sep__6_06:05:47_2015_modification_0.pdb.gz
INFO:: replace_coords: 18 atoms updated.
Symmetry available for this molecule
created 11 bond restraints
created 15 angle restraints
created 1 plane restraints
created 1 chiral vol restraints
created 28 restraints
INFO:: make_restraints(): made 39 non-bonded restraints
initial distortion_score: 4023
Initial RMS Z values
bonds: 1.152
angles: 0.8476
torsions: N/A
planes: 3.056
non-bonded: 116.2
chiral vol: 0.7578
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 23) at -476.8
Final Estimated RMS Z Scores:
bonds: 0.4633
angles: 0.3586
torsions: N/A
planes: 0.3184
non-bonded: 0.02421
chiral vol: 0.04958
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 11.83
Refinement elapsed time: 0.022
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_0.pdb.gz
INFO:: replace_coords: 12 atoms updated.
created 12 bond restraints
created 15 angle restraints
created 1 plane restraints
created 1 chiral vol restraints
created 29 restraints
INFO:: make_restraints(): made 36 non-bonded restraints
initial distortion_score: 3147
Initial RMS Z values
bonds: 17.39
angles: 0.3586
torsions: N/A
planes: 0.3184
non-bonded: 0
chiral vol: 0.04958
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 15) at -543.4
Final Estimated RMS Z Scores:
bonds: 0.1298
angles: 0.1781
torsions: N/A
planes: 0.4242
non-bonded: 0
chiral vol: 0.09939
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 11.86
Refinement elapsed time: 0.019
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_1.pdb.gz
INFO:: replace_coords: 12 atoms updated.
INFO:: wrote mmCIF "coot-test-ala.cif"
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ACT.cif
There are 2 data in /lmb/home/pemsley/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: 0.03181
angles: 0.1912
torsions: N/A
planes: 0.03549
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 12.32
Refinement elapsed time: 0.034
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-ACT.pdb_Sun_Sep__6_06:05:47_2015_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 53 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_0.pdb.gz
istat: ; 1
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_1.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 26 A 27
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_2.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_3.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_4.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_5.pdb.gz
INFO:: Removing CIS peptide from PDB header: B 26 B 27
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_2015_modification_6.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:47_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_06:05:48_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:48_2015_modification_0.pdb.gz
INFO:: replace_coords: 1465 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:48_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: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 57 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%]
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb
PDB file /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 50/87
Molecule 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
> /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb
---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID
> target seq:
DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
INFO:: alignment score 163.5
DEBUG:: s.length() 95
DEBUG:: nSelResidues 87
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Sun_Sep__6_06:05:49_2015_modification_0.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 26 A 27
The alignment resulted in the following
Insertions (coalesced):
from 1 to 4 ASP VAL SER
from 11 to 14 LEU PRO PRO
from 62 to 64 PRO GLY
Insertions (singles):
[spec: 4 "A" 1 ""] -> ASP
[spec: 4 "A" 2 ""] -> VAL
[spec: 4 "A" 3 ""] -> SER
[spec: 4 "A" 11 ""] -> LEU
[spec: 4 "A" 12 ""] -> PRO
[spec: 4 "A" 13 ""] -> PRO
[spec: 4 "A" 62 ""] -> PRO
[spec: 4 "A" 63 ""] -> GLY
Deletions:
[spec: 4 "A" 24 ""]
[spec: 4 "A" 33 ""]
Mutations:
apply resno updates...
Applied 3 insertions
Applied 0 mutations
Applied 2 deletions
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 59 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:49_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 60 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:50_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3hfl.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb3hfl.ent has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: NCS chain comparison 15/212
INFO:: NCS chain comparison 7/212
INFO:: NCS chain comparison 10/215
Molecule 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PCA.cif
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz
Number of OBSERVED reflections: 17920
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 64, 96, 90)
INFO:: 0.019 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.01 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 2.004e-11
Map sigma: ....... 0.2604
Map maximum: ..... 1.718
Map minimum: ..... -1.034
INFO:: 0.007 seconds for contour map
INFO:: 0.039 seconds in total
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Sun_Sep__6_06:05:50_2015_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Fitting score for best rotamer: 5.834
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Sun_Sep__6_06:05:50_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_06:05:50_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Sun_Sep__6_06:05:50_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_06:05:50_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Sun_Sep__6_06:05:50_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_06:05:50_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_06:05:50_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_06:05:50_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_06:05:50_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_06:05:50_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_06:05:51_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Sun_Sep__6_06:05:51_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_06:05:51_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_06:05:51_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_06:05:51_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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:51_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb
PDB file /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 68 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_some-waters-with-ter.pdb_Sun_Sep__6_06:05:51_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: /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb
PDB file /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 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: 1.5 3.6
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 49 waters in water fitting
Done - back from lig.water_fit()
DEBUG:: new_waters_mol_flag: 0
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tm+some-waters.pdb_Sun_Sep__6_06:05:52_2015_modification_0.pdb.gz
INFO:: Adding to solvent chain: D
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 70 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:52_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: /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb
PDB file /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 71 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_water-test-no-cell.pdb_Sun_Sep__6_06:05:57_2015_modification_0.pdb.gz
No symmetry available
INFO:: moved 0 water molecules
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb
PDB file /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 72 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pathological-water-test.pdb_Sun_Sep__6_06:05:58_2015_modification_0.pdb.gz
INFO:: moved 181 water molecules
Symmetry available for this molecule
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 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: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.021 seconds for contour map
INFO:: 0.07 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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:58_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__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:05:58_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 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: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
INFO:: fill_ghost_info Constructed 3 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TAR.cif
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 78 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NPO.cif
-X,-X+Y,-Z+1/3 ->
-1 0 0
-1 1 0
0 0 -1
translations: 0 0 0.3333
pre-trans: 0 0 0
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Matching/moving molecule number 82 to 81
INFO:: LSQ matched 4 atoms
INFO:: 4 matched atoms had:
mean devi: 0.03532
rms devi: 0.03779
max devi: 0.05453
min devi: 0.01668
INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076)
INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:00_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: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 83 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 91/204
INFO:: NCS chain comparison 90/204
INFO:: NCS chain comparison 175/179
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain C onto Chain B"
Molecule 84 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: spacegroup: P 21 21 21
INFO:: spacegroup: C 1 2 1
INFO:: Matching/moving molecule number 83 to 84
INFO:: LSQ matched 164 atoms
INFO:: 164 matched atoms had:
mean devi: 0.5023
rms devi: 0.5938
max devi: 1.679
min devi: 0.04318
INFO:: Axis orientation: ( 0.567, -0.7175, 0.4046)
INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:00_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: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 85 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:01_2015_modification_0.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 86 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2goz-manip.pdb
PDB file /lmb/home/pemsley/data/greg-data/2goz-manip.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 7 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/85
Molecule 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GDP.cif
INFO:: using standard CCP4 Refmac dictionary to search for "Gr"
INFO:: using standard CCP4 Refmac dictionary to search for "Ar"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/AR.cif
INFO:: using standard CCP4 Refmac dictionary to search for "Ur"
INFO:: using standard CCP4 Refmac dictionary to search for "Cr"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CR.cif
INFO:: using standard CCP4 Refmac dictionary to search for "OMC"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/o/OMC.cif
INFO:: using standard CCP4 Refmac dictionary to search for "5BU"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/5/5BU.cif
SFAC LINE: SFAC C H N O S
INFO:: CELL set to 5.903 13.7 9.237 90 98.21 90
READ-INS:: Spacegroup: "P 1 21/c 1"
INFO:: chain has 2 residues
Symmetry available for this molecule
Molecule 88 read successfully
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O CO
INFO:: CELL set to 34.32 34.32 11.09 90 90 90
READ-INS:: Spacegroup: "I 41 2 2"
INFO:: chain has 2 residues
Symmetry available for this molecule
Molecule 89 read successfully
INFO:: spacegroup: I 41 2 2
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O S
INFO:: CELL set to 77.73 77.73 77.73 90 90 90
READ-INS:: Spacegroup: "I 21 3"
INFO:: chain has 121 residues
Symmetry available for this molecule
Molecule 90 read successfully
ll: 24
DEBUG:: space group initialised with symbol "I 21 3"
in read_data_sm_cif() cell is Cell (77.726,77.726,77.726, 90, 90, 90)
in read_data_sm_cif() spg is I 21 3
in read_data_sm_cif() reso is 0.5889
Map statistics: mean: -5.07e-05 st.d: 0.3052
Map statistics: min: -0.781, max: 6.079
-0.6953 231
-0.5238 4724
-0.3523 24910
-0.1808 55291
-0.00927 95241
0.1622 40930
0.3337 7480
0.5052 3968
0.6767 2790
0.8482 2117
1.02 1738
1.191 1221
1.363 888
1.534 595
1.706 355
1.877 240
2.049 137
2.22 97
2.392 62
2.563 46
2.735 17
2.906 17
3.078 13
3.249 10
3.421 7
3.592 1
3.764 3
3.935 7
4.107 2
4.278 5
4.45 1
4.621 2
4.793 2
4.964 0
5.136 1
5.307 0
5.479 0
5.65 0
5.822 0
5.993 1
6.165 0
Map statistics: mean: -1.005e-05 st.d: 0.04681
Map statistics: min: -0.2115, max: 0.6486
-0.2008 7
-0.1793 48
-0.1578 209
-0.1363 787
-0.1148 2257
-0.09325 5676
-0.07175 12730
-0.05025 24380
-0.02874 38191
-0.007239 46229
0.01427 43880
0.03577 32484
0.05727 19420
0.07878 9718
0.1003 4120
0.1218 1677
0.1433 718
0.1648 329
0.1863 133
0.2078 77
0.2293 29
0.2508 11
0.2723 13
0.2938 8
0.3153 2
0.3368 2
0.3583 2
0.3798 1
0.4013 1
0.4228 2
0.4443 2
0.4658 1
0.4873 1
0.5088 1
0.5304 1
0.5519 1
0.5734 0
0.5949 0
0.6164 0
0.6379 2
0.6594 0
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
WARNING:: invalid molecule (204050) for write_shelx_ins_file
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " N "
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CA "
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CB "
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " CG "
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD1"
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " OD2"
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " C "
WARNING:: failed to get AFIX handle for "A" 1 "ASP" " O "
WARNING:: failed to get AFIX handle for "A" 2 "VAL" " N "
WARNING:: failed to get AFIX handle for "A" 2 "VAL" " CA "
INFO:: SHELXL file rnase.ins written.
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Masking around 32 atoms
fitting terminal residue with 100 random trials
INFO:: Fitting terminal residue without individual rigid body fitting.
B 2021 ALA N :: xyz = ( -11.33, 19.47, 57.91)
B 2021 ALA C :: xyz = ( -12.04, 20.27, 60.12)
B 2021 ALA CA :: xyz = ( -11.37, 20.62, 58.8)
B 2021 ALA O :: xyz = ( -11.44, 20.43, 61.19)
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/atom_selection_from_insulin.res_Sun_Sep__6_06:06:02_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/_lmb_home_pemsley_data_greg-data_insulin.res_Sun_Sep__6_06:06:02_2015_modification_0.res
1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule
INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56)
using sigma cut off 0.6
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.3052
INFO:: Using density cut-off: 0.1831 (0.6 sigma) (mean -0.02035 stdev: 0.1119)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 1.5 3.6
INFO:: Finding clusters...done
-------------------------------------------------------------
INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water
INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water
INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water
INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water
INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water
INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water
INFO:: found 126 waters in water fitting
Done - back from lig.water_fit()
DEBUG:: new_waters_mol_flag: 0
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Sun_Sep__6_06:06:02_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
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: 2.83656828122208:
pass intermediate 2.8 tolerance test
OK plane atom " CB "
Bond-length: 1.51580697715372:
PASS: update monomer restraints
Entered testcase - Write mmCIF restraints correctly
PASS: Write mmCIF restraints correctly
Entered testcase - Refinement OK with zero bond esd
PASS: Refinement OK with zero bond esd
Entered testcase - Change Chain IDs and Chain Sorting
PASS: Change Chain IDs and Chain Sorting
Entered testcase - Replace Fragment
distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327)
PASS: Replace Fragment
Entered testcase - Residues in Region of Residue
found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 ""))
found 0 neighbours ()
PASS: Residues in Region of Residue
Entered testcase - Residues in region of a point
PASS: Residues in region of a point
Entered testcase - Empty molecule on type selection
PASS: Empty molecule on type selection
Entered testcase - Set Rotamer
PASS: Set Rotamer
Entered testcase - Rotamer names and scores are correct
Rotamer 0 : "m-85" 100.0
Rotamer 1 : "t80" 90.1668395996094
Rotamer 2 : "p90" 50.7077865600586
Rotamer 3 : "m -30 " 21.4231548309326
Rotamer 4 : "m -30 " 21.4231548309326
PASS: Rotamer names and scores are correct
Entered testcase - Align and mutate a model with deletions
::::: (58 "A" 1 "") #f #f
::::: (58 "A" 4 "") #t #t
::::: (58 "A" 59 "") #t #t
::::: (58 "A" 60 "") #f #f
::::: (58 "A" 61 "") #f #f
::::: (58 "A" 92 "") #t #t
::::: (58 "A" 94 "") #f #f
PASS: Align and mutate a model with deletions
Entered testcase - renumbered residues should be in seqnum order
PASS: renumbered residues should be in seqnum order
Entered testcase - Autofit Rotamer on Residues with Insertion codes
PASS: Autofit Rotamer on Residues with Insertion codes
Entered testcase - RNA base has correct residue type after mutation
mutated base to type "C" - was "A"
mutated base to type "Cr" - was "A"
PASS: RNA base has correct residue type after mutation
Entered testcase - resname from serial number doesnt crash on silly input
PASS: resname from serial number doesnt crash on silly input
Entered testcase - DNA bases are the correct residue type after mutation
mutated base to type "DC"
mutated base to type "DG"
mutated base to type "DA"
mutated base to type "DT"
mutated base to type "Cd"
mutated base to type "Gd"
mutated base to type "Ad"
mutated base to type "Td"
PASS: DNA bases are the correct residue type after mutation
Entered testcase - SegIDs are correct after mutate
PASS: SegIDs are correct after mutate
Entered testcase - TER on water chain is removed on adding a water by hand
PASS: TER on water chain is removed on adding a water by hand
Entered testcase - TER on water chain is removed on adding waters automatically
PASS: TER on water chain is removed on adding waters automatically
Entered testcase - Adding atoms to Many-Chained Molecule
PASS: Adding atoms to Many-Chained Molecule
Entered testcase - Arrange waters round protein
PASS: Arrange waters round protein
Entered testcase - Correct Segid After Add Terminal Residue
PASS: Correct Segid After Add Terminal Residue
Entered testcase - Correct Segid after NCS residue range copy
PASS: Correct Segid after NCS residue range copy
Entered testcase - Merge Water Chains
PASS: Merge Water Chains
Entered testcase - Consolidated merge
-------- starting chain list -----------
DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "")
DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K")
PASS: Consolidated merge
Entered testcase - LSQ by atom
PASS: LSQ by atom
Entered testcase - LSQing changes the space-group and cell to that of the reference molecule
PASS: LSQing changes the space-group and cell to that of the reference molecule
Entered testcase - set-residue-name sets the correct residue
PASS: set-residue-name sets the correct residue
Entered testcase - fit-protein-make-specs makes all specs
specs: 189 ((86 "A" 1 "") (86 "A" 2 "") (86 "A" 3 "") (86 "A" 4 "") (86 "A" 5 "") (86 "A" 6 "") (86 "A" 7 "") (86 "A" 8 "") (86 "A" 9 "") (86 "A" 10 "") (86 "A" 11 "") (86 "A" 12 "") (86 "A" 13 "") (86 "A" 14 "") (86 "A" 15 "") (86 "A" 16 "") (86 "A" 17 "") (86 "A" 18 "") (86 "A" 19 "") (86 "A" 20 "") (86 "A" 21 "") (86 "A" 22 "") (86 "A" 23 "") (86 "A" 24 "") (86 "A" 25 "") (86 "A" 26 "") (86 "A" 27 "") (86 "A" 28 "") (86 "A" 29 "") (86 "A" 30 "") (86 "A" 31 "") (86 "A" 32 "") (86 "A" 33 "") (86 "A" 34 "") (86 "A" 35 "") (86 "A" 36 "") (86 "A" 37 "") (86 "A" 38 "") (86 "A" 39 "") (86 "A" 40 "") (86 "A" 41 "") (86 "A" 42 "") (86 "A" 43 "") (86 "A" 44 "") (86 "A" 45 "") (86 "A" 46 "") (86 "A" 47 "") (86 "A" 48 "") (86 "A" 49 "") (86 "A" 50 "") (86 "A" 51 "") (86 "A" 52 "") (86 "A" 53 "") (86 "A" 54 "") (86 "A" 55 "") (86 "A" 56 "") (86 "A" 57 "") (86 "A" 58 "") (86 "A" 59 "") (86 "A" 60 "") (86 "A" 61 "") (86 "A" 62 "") (86 "A" 63 "") (86 "A" 64 "") (86 "A" 65 "") (86 "A" 66 "") (86 "A" 67 "") (86 "A" 68 "") (86 "A" 69 "") (86 "A" 70 "") (86 "A" 71 "") (86 "A" 72 "") (86 "A" 73 "") (86 "A" 74 "") (86 "A" 75 "") (86 "A" 76 "") (86 "A" 77 "") (86 "A" 78 "") (86 "A" 79 "") (86 "A" 80 "") (86 "A" 81 "") (86 "A" 82 "") (86 "A" 83 "") (86 "A" 84 "") (86 "A" 85 "") (86 "A" 86 "") (86 "A" 87 "") (86 "A" 88 "") (86 "A" 89 "") (86 "A" 90 "") (86 "A" 91 "") (86 "A" 92 "") (86 "A" 93 "") (86 "B" 1 "") (86 "B" 2 "") (86 "B" 3 "") (86 "B" 4 "") (86 "B" 5 "") (86 "B" 6 "") (86 "B" 7 "") (86 "B" 8 "") (86 "B" 9 "") (86 "B" 10 "") (86 "B" 11 "") (86 "B" 12 "") (86 "B" 13 "") (86 "B" 14 "") (86 "B" 15 "") (86 "B" 16 "") (86 "B" 17 "") (86 "B" 18 "") (86 "B" 19 "") (86 "B" 20 "") (86 "B" 21 "") (86 "B" 22 "") (86 "B" 23 "") (86 "B" 24 "") (86 "B" 25 "") (86 "B" 26 "") (86 "B" 27 "") (86 "B" 28 "") (86 "B" 29 "") (86 "B" 30 "") (86 "B" 31 "") (86 "B" 32 "") (86 "B" 33 "") (86 "B" 34 "") (86 "B" 35 "") (86 "B" 36 "") (86 "B" 37 "") (86 "B" 38 "") (86 "B" 39 "") (86 "B" 40 "") (86 "B" 41 "") (86 "B" 42 "") (86 "B" 43 "") (86 "B" 44 "") (86 "B" 45 "") (86 "B" 46 "") (86 "B" 47 "") (86 "B" 48 "") (86 "B" 49 "") (86 "B" 50 "") (86 "B" 51 "") (86 "B" 52 "") (86 "B" 53 "") (86 "B" 54 "") (86 "B" 55 "") (86 "B" 56 "") (86 "B" 57 "") (86 "B" 58 "") (86 "B" 59 "") (86 "B" 60 "") (86 "B" 61 "") (86 "B" 62 "") (86 "B" 63 "") (86 "B" 64 "") (86 "B" 65 "") (86 "B" 66 "") (86 "B" 67 "") (86 "B" 68 "") (86 "B" 69 "") (86 "B" 70 "") (86 "B" 71 "") (86 "B" 72 "") (86 "B" 73 "") (86 "B" 74 "") (86 "B" 75 "") (86 "B" 76 "") (86 "B" 77 "") (86 "B" 78 "") (86 "B" 79 "") (86 "B" 80 "") (86 "B" 81 "") (86 "B" 82 "") (86 "B" 83 "") (86 "B" 84 "") (86 "B" 85 "") (86 "B" 86 "") (86 "B" 87 "") (86 "B" 88 "") (86 "B" 89 "") (86 "B" 90 "") (86 "B" 91 "") (86 "B" 92 "") (86 "B" 93 "") (86 "B" 94 "") (86 "B" 95 "") (86 "B" 96 ""))
PASS: fit-protein-make-specs makes all specs
Entered testcase - Phosphate distance in pucker analysis is sane
PASS: Phosphate distance in pucker analysis is sane
Ended 01-pdb+mtz.scm
Running 02-shelx.scm ...
Entered testcase - Read small molecule .res file
PASS: Read small molecule .res file
Entered testcase - Read hollander small molecule .res file
PASS: Read hollander small molecule .res file
Entered testcase - read shelx insulin with fcf
PASS: read shelx insulin with fcf
Entered testcase - Write an INS from PDB test
PASS: Write an INS from PDB test
Entered testcase - new molecule by atom selection inherits shelx molecule flag
PASS: new molecule by atom selection inherits shelx molecule flag
Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy
PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy
Entered testcase - Add water to SHELX molecule
PASS: Add water to SHELX molecule
Entered testcase - Find Waters for a SHELXL molecule
PASS: Find Waters for a SHELXL molecule
Entered testcase - NPD Anisotropic Atom [Mitch Miller]
PASS: NPD Anisotropic Atom [Mitch Miller]
Entered testcase - close shelx molecules
PASS: close shelx molecules
Entered testcase - Aniso Bs in P21
b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018)
b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018)
PASS: Aniso Bs in P21
Entered testcase - Don't crash on reading a strange HAT file
PASS: Don't crash on reading a strange HAT file
Ended 02-shelx.scm
Running 03-ligand.scm ...
Entered testcase - Get monomer test
run-command-in-dir dir: "coot-ccp4/" exe: "libcheck" cl-args: () data-lines: ("N" "MON 3GP" "") log-file-name: "coot-libcheck-3GP.log" #t
:
: --- LIBCHECK --- /Vers 5.2.02 ; 02.12.2014/
:
:
: Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/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: <Y>/A/N - Y - hydrogen atoms where they are
: # A - with all hydrogen atoms
: # N - without hydrogen atoms
: #IND: <N>/Y - Y - create index of mon_lib.cif
: # output file: "new_mon_lib_ind.cif"
: #FILE_O: <libcheck > - 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: <M>/S/L - S short output, L - long, M - medium
: #REF: <Y>/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: <N>/Y - use Vobs from coords instead Videal
: #LCOOR: <Y>/N - Y use coords from lib description
: #NODIST: <N>/Y - Y not read the distributed library
: # (only with FILE_L)
: #SRCH: <N>/Y/0 - Y - global search, 0 - for MON from PDB_file
: # (only with NODIST = N)
:
: #--- type "keyword parameters" and/or ---
: #--- press key "CR" to run program ---
: --> --> MON : 3GP
: -------------
: -------------
: Keywords:
: HFLAG : Y
: COOR : N
: LCOOR : Y
: SRCH : N
: REF : Y
: NODIST: N
: ------------------------------
: --- LIBRARY OF MONOMERS ---
: _lib_name mon_lib
: _lib_version 5.44
: _lib_update 30/05/14
: ------------------------------
: NUMBER OF MONOMERS IN THE LIBRARY : 11608
: with complete description : 11608
: NUMBER OF MODIFICATIONS : 63
: NUMBER OF LINKS : 73
: I am reading libraries. Please wait.
: - energy parameters
: - monomer"s description (links & mod )
: I am reading library. Please wait.
: - monomer"s description
: WARNING: bond C4' - C3' delta (lib-coord) : 0.020
: WARNING: bond C3' - C2' delta (lib-coord) : 0.023
: WARNING: bond N9 - C8 delta (lib-coord) : 0.028
: WARNING: bond N9 - C4 delta (lib-coord) : 0.030
: WARNING: bond C8 - N7 delta (lib-coord) : 0.050
: WARNING: bond C5 - C6 delta (lib-coord) : 0.075
: WARNING: bond C5 - C4 delta (lib-coord) : 0.090
: WARNING: bond C6 - O6 delta (lib-coord) : 0.031
: WARNING: bond C2 - N1 delta (lib-coord) : 0.027
: WARNING: bond N3 - C2 delta (lib-coord) : 0.036
: WARNING: angle O4' - C1' - C2' delta (lib-coord) : 4.463
: WARNING: angle C1' - O4' - C4' delta (lib-coord) : 6.546
: WARNING: angle C1' - C2' - C3' delta (lib-coord) : 7.042
: WARNING: angle C2' - C3' - C4' delta (lib-coord) : 6.948
: WARNING: angle C3' - O3' - P delta (lib-coord) : 13.628
: WARNING: angle O3P - P - O2P delta (lib-coord) : 10.426
: WARNING: angle O3P - P - O1P delta (lib-coord) : 10.379
: WARNING: angle O2P - P - O1P delta (lib-coord) : 10.383
: WARNING: angle C3' - C4' - O4' delta (lib-coord) : 4.651
: WARNING: tors O6 - C6 - N1 - C2 delta (lib-coord) : 0.303
: WARNING: tors C6 - N1 - C2 - N3 delta (lib-coord) : 0.636
: WARNING: tors N1 - C2 - N2 - HN21 delta (lib-coord) : 0.000
: WARNING: tors N1 - C2 - N3 - C4 delta (lib-coord) : 0.332
: WARNING: tors C2 - N3 - C4 - N9 delta (lib-coord) : 0.079
: WARNING: tors N3 - C4 - C5 - N7 delta (lib-coord) : 0.034
: WARNING: tors C4 - C5 - C6 - O6 delta (lib-coord) : 0.034
: WARNING: tors C4 - C5 - N7 - C8 delta (lib-coord) : 0.020
: WARNING: tors N3 - C4 - N9 - C1' delta (lib-coord) : 0.059
: WARNING: tors C4 - N9 - C8 - N7 delta (lib-coord) : 0.034
: * CIFile : libcheck_3GP.cif
: * PDBfile : libcheck_3GP.pdb
: * Plotfile: libcheck_3GP.ps
: Output dictionary
: mmcif : libcheck.lib
: odb : libcheck.odb
INFO:: libcheck status: 0
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:<html> <!-- CCP4 HTML LOGFILE -->
:<hr>
:<!--SUMMARY_END--></FONT></B>
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:<pre>
:
: ###############################################################
: ###############################################################
: ###############################################################
: ### CCP4 6.5.016: Refmac_5.8.0131 version 5.8.0131 : 06/08/15##
: ###############################################################
: User: pemsley Run date: 6/ 9/2015 Run time: 06:06:05
:
:
: Please reference: Collaborative Computational Project, Number 4. 2011.
: "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
: as well as any specific reference in the program write-up.
:
:<!--SUMMARY_END--></FONT></B>
: $TEXT:Reference1: $$ Main reference $$
: "REFMAC5 for the refinement of macromolecular crystal structures:"
: G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011)
: Acta Crystallogr. D67, 355-367
:
: $$
: $SUMMARY :Reference1: $$ Refmac: $$
: :TEXT:Reference1: $$
:
: $TEXT:Reference2: $$ Secondary reference $$
: "Refinement of Macromolecular Structures by the Maximum-Likelihood Method:"
: G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
: Acta Crystallogr. D53, 240-255
: EU Validation contract: BIO2CT-92-0524
:
: $$
: $SUMMARY :Reference2: $$ Refmac: $$
: :TEXT:Reference2: $$
:
: Data line--- MODE NEWENTRY
: Data line--- END
: Data line--- MODE NEWENTRY
: Data line--- END
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
:
: **** Input and Default parameters# ****
:
:
:Input coordinate file. Logical name - XYZIN actual file name - coot-ccp4/libcheck_3GP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name - coot-ccp4/monomer-3GP.pdb
:
: Refinement type : Idealisation
:
: **** Makecif parameters ****
:
:Dictionary files for restraints : /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ener_lib.cif
:User supplied dictionary entries: coot-ccp4/libcheck_3GP.cif
: Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
: Hydrogens will be restored in their riding positions
: hydrogens will be written to the output file
: Links between monomers will be checked. Only those links present in the coordinate file will be used
: Standard sugar links will be analysed and used
: For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
: Symmetry related links will be analysed and used
: Cis peptides will be found and used automatically
:
:
:
:
:Monitoring style is "MEDIUM". Complete information will be printed out in the
:first and last cycle. In all other cycles minimum information will be printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will be printed out
:Distance outliers 10.000
:Angle outliers 10.000
:Torsion outliers 10.000
:Chiral volume outliers 10.000
:Plane outliers 10.000
:Non-bonding outliers 10.000
:---------------------------------------------------------------
:
: Input file :coot-ccp4/libcheck_3GP.pdb
: ------------------------------
: --- LIBRARY OF MONOMERS ---
: _lib_name mon_lib
: _lib_version 5.44
: _lib_update 30/05/14
: ------------------------------
: NUMBER OF MONOMERS IN THE LIBRARY : 11608
: with complete description : 11608
: NUMBER OF MODIFICATIONS : 63
: NUMBER OF LINKS : 73
: I am reading libraries. Please wait.
: - energy parameters
: - monomer"s description (links & mod )
:
:FORMATTED OLD file opened on unit 45
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:Logical name: ATOMSF, Filename: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/atomsf.lib
:<!--SUMMARY_END--></FONT></B>
:
: WARNING: "SCALE" card is absent in input PDB file
: Number of atoms : 24
: Number of residues : 1
: Number of chains : 1
: I am reading library. Please wait.
: mon_lib.cif
: --------------------------------
: --- title of input coord file ---
:
: PDB_code:3GP
: PDB_name:coords of 3GP from prog: libcheck
: PDB_date:XX-XXX-XX
: --------------------------------
: Number of chains : 1
: Total number of monomers : 1
: Number of atoms : 36
: Number of missing atoms : 0
: Number of rebuilt atoms : 12
: Number of unknown atoms : 0
: Number of deleted atoms : 0
:
:
: loop_
: _atom_type_symbol
: _atom_type_scat_Cromer_Mann_a1
: _atom_type_scat_Cromer_Mann_b1
: _atom_type_scat_Cromer_Mann_a2
: _atom_type_scat_Cromer_Mann_b2
: _atom_type_scat_Cromer_Mann_a3
: _atom_type_scat_Cromer_Mann_b3
: _atom_type_scat_Cromer_Mann_a4
: _atom_type_scat_Cromer_Mann_b4
: _atom_type_scat_Cromer_Mann_c
:
:
: O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508
: C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156
: N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290
: H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030
: P 6.4345 1.9067 4.1791 27.1570 1.7800 0.5260 1.4908 68.1645 1.1149
:
:
: Number of distances : 0
: Number of angles : 0
: Number of torsions : 0
: Number of planes : 0
: Number of chirals : 0
: Number of intervals : 0
:--------------------------------------------------------------------------------
:--------------------------------------------------------------------------------
: Standard External All
: Bonds: 36 0 36
: Angles: 64 0 64
: Chirals: 4 0 4
: Planes: 2 0 2
: Torsions: 20 0 20
: Intervals: 0 0 0
:--------------------------------------------------------------------------------
:
:
: Number of harmonic restraints = 0
: Number of atoms in special position = 0
: -----------------------------------------------------
:
: chir max = 0.0000000
: chir_max = 0.0000000 3.0000000 5.0000000
:
:
: CGMAT cycle number = 1
:
: function value 101.82433
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.030 0.020
:Bond distances: others 10 0.001 0.020
:Bond angles : refined atoms 40 4.292 3.000
:Bond angles : others 24 1.625 3.000
:Chiral centres: refined atoms 4 0.186 0.200
:Planar groups: refined atoms 14 0.002 0.020
:Planar groups: others 6 0.005 0.020
:VDW repulsions.others 12 0.183 0.200
:VDW; torsion: refined_atoms 14 0.281 0.200
:VDW; torsion.others 12 0.178 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.0000000
: Not converging with gamma equal 0.0000000
: Trying gamma equal 5.24999984E-02
: Gamma decreased to 4.19999994E-02
:
:
: fvalues 0.0000000 101.82433 36.313282 101.82433
:
:
: CGMAT cycle number = 2
:
: function value 36.313282
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.010 0.020
:Bond distances: others 10 0.002 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19999994E-02
: Gamma decreased to 3.24545428E-02
:
:
: fvalues 0.0000000 36.313282 32.770733 36.313282
:
:
: CGMAT cycle number = 3
:
: function value 32.770733
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 3.24545428E-02
: Gamma decreased to 2.37768572E-02
:
:
: fvalues 0.0000000 32.770733 32.165546 32.770733
:
:
: CGMAT cycle number = 4
:
: function value 32.165546
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 2.37768572E-02
: Gamma decreased to 1.58880539E-02
:
:
: fvalues 0.0000000 32.165546 31.749023 32.165546
:
:
: CGMAT cycle number = 5
:
: function value 31.749023
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 1.58880539E-02
: Not converging with gamma equal 1.58880539E-02
: Trying gamma equal 5.35391644E-02
: Gamma decreased to 4.60089408E-02
:
:
: fvalues 0.0000000 31.749023 31.600889 31.749023
:
:
: CGMAT cycle number = 6
:
: function value 31.600889
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.60089408E-02
: Not converging with gamma equal 4.60089408E-02
: Trying gamma equal 8.19486380E-02
: Not converging with gamma equal 8.19486380E-02
: Trying gamma equal 0.11968531
: Gamma decreased to 0.11213798
:
:
: fvalues 0.0000000 31.600889 31.536364 31.600889
:
:
: CGMAT cycle number = 7
:
: function value 31.536364
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 0.11213798
: Gamma decreased to 0.10527676
:
:
: fvalues 0.0000000 31.536364 31.471638 31.536364
:
:
: CGMAT cycle number = 8
:
: function value 31.471638
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 0.10527676
: Gamma decreased to 9.90392938E-02
:
:
: fvalues 0.0000000 31.471638 31.406364 31.471638
:
:
: CGMAT cycle number = 9
:
: function value 31.406364
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 9.90392938E-02
: Gamma decreased to 9.33688730E-02
:
:
: fvalues 0.0000000 31.406364 31.340563 31.406364
:
:
: CGMAT cycle number = 10
:
: function value 31.340563
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 9.33688730E-02
: Gamma decreased to 8.82139429E-02
:
:
: fvalues 0.0000000 31.340563 31.274326 31.340563
:
:
: CGMAT cycle number = 11
:
: function value 31.274326
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.82139429E-02
: Gamma decreased to 8.35276395E-02
:
:
: fvalues 0.0000000 31.274326 31.207850 31.274326
:
:
: CGMAT cycle number = 12
:
: function value 31.207850
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.35276395E-02
: Gamma decreased to 7.92673677E-02
:
:
: fvalues 0.0000000 31.207850 31.141224 31.207850
:
:
: CGMAT cycle number = 13
:
: function value 31.141224
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.92673677E-02
: Gamma decreased to 7.53943920E-02
:
:
: fvalues 0.0000000 31.141224 31.074661 31.141224
:
:
: CGMAT cycle number = 14
:
: function value 31.074661
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.53943920E-02
: Gamma decreased to 7.18735084E-02
:
:
: fvalues 0.0000000 31.074661 31.008284 31.074661
:
:
: CGMAT cycle number = 15
:
: function value 31.008284
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.18735084E-02
: Gamma decreased to 6.86727017E-02
:
:
: fvalues 0.0000000 31.008284 30.942270 31.008284
:
:
: CGMAT cycle number = 16
:
: function value 30.942270
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.86727017E-02
: Gamma decreased to 6.57628775E-02
:
:
: fvalues 0.0000000 30.942270 30.876766 30.942270
:
:
: CGMAT cycle number = 17
:
: function value 30.876766
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.57628775E-02
: Not converging with gamma equal 6.57628775E-02
: Trying gamma equal 7.96506703E-02
: Gamma decreased to 7.68731087E-02
:
:
: fvalues 0.0000000 30.876766 30.822355 30.876766
:
:
: CGMAT cycle number = 18
:
: function value 30.822355
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.68731087E-02
: Gamma decreased to 7.43480548E-02
:
:
: fvalues 0.0000000 30.822355 30.768475 30.822355
:
:
: CGMAT cycle number = 19
:
: function value 30.768475
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.43480548E-02
: Gamma decreased to 7.20525533E-02
:
:
: fvalues 0.0000000 30.768475 30.715254 30.768475
:
:
: CGMAT cycle number = 20
:
: function value 30.715254
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.20525533E-02
: Gamma decreased to 6.99657351E-02
:
:
: fvalues 0.0000000 30.715254 30.662777 30.715254
:
:
: CGMAT cycle number = 21
:
: function value 30.662777
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.99657351E-02
: Gamma decreased to 6.80686235E-02
:
:
: fvalues 0.0000000 30.662777 30.611145 30.662777
:
:
: CGMAT cycle number = 22
:
: function value 30.611145
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.80686235E-02
: Gamma decreased to 6.63439780E-02
:
:
: fvalues 0.0000000 30.611145 30.560417 30.611145
:
:
: CGMAT cycle number = 23
:
: function value 30.560417
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.63439780E-02
: Gamma decreased to 6.47761226E-02
:
:
: fvalues 0.0000000 30.560417 30.510704 30.560417
:
:
: CGMAT cycle number = 24
:
: function value 30.510704
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.47761226E-02
: Gamma decreased to 6.33507967E-02
:
:
: fvalues 0.0000000 30.510704 30.462093 30.510704
:
:
: CGMAT cycle number = 25
:
: function value 30.462093
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.33507967E-02
: Not converging with gamma equal 6.33507967E-02
: Trying gamma equal 7.01534897E-02
: Gamma decreased to 6.87929541E-02
:
:
: fvalues 0.0000000 30.462093 30.418858 30.462093
:
:
: CGMAT cycle number = 26
:
: function value 30.418858
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.87929541E-02
: Gamma decreased to 6.75560981E-02
:
:
: fvalues 0.0000000 30.418858 30.376587 30.418858
:
:
: CGMAT cycle number = 27
:
: function value 30.376587
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.75560981E-02
: Gamma decreased to 6.64316863E-02
:
:
: fvalues 0.0000000 30.376587 30.335243 30.376587
:
:
: CGMAT cycle number = 28
:
: function value 30.335243
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.64316863E-02
: Gamma decreased to 6.54094964E-02
:
:
: fvalues 0.0000000 30.335243 30.294954 30.335243
:
:
: CGMAT cycle number = 29
:
: function value 30.294954
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.54094964E-02
: Gamma decreased to 6.44802302E-02
:
:
: fvalues 0.0000000 30.294954 30.255678 30.294954
:
:
: CGMAT cycle number = 30
:
: function value 30.255678
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.44802302E-02
: Gamma decreased to 6.36354461E-02
:
:
: fvalues 0.0000000 30.255678 30.217442 30.255678
:
:
: CGMAT cycle number = 31
:
: function value 30.217442
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.36354461E-02
: Gamma decreased to 6.28674552E-02
:
:
: fvalues 0.0000000 30.217442 30.180283 30.217442
:
:
: CGMAT cycle number = 32
:
: function value 30.180283
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.28674552E-02
: Gamma decreased to 6.21692836E-02
:
:
: fvalues 0.0000000 30.180283 30.144108 30.180283
:
:
: CGMAT cycle number = 33
:
: function value 30.144108
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.21692836E-02
: Gamma decreased to 6.15345836E-02
:
:
: fvalues 0.0000000 30.144108 30.109032 30.144108
:
:
: CGMAT cycle number = 34
:
: function value 30.109032
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.15345836E-02
: Gamma decreased to 6.09575808E-02
:
:
: fvalues 0.0000000 30.109032 30.074951 30.109032
:
:
: CGMAT cycle number = 35
:
: function value 30.074951
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.09575808E-02
: Gamma decreased to 6.04330339E-02
:
:
: fvalues 0.0000000 30.074951 30.041904 30.074951
:
:
: CGMAT cycle number = 36
:
: function value 30.041904
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.04330339E-02
: Gamma decreased to 5.99561743E-02
:
:
: fvalues 0.0000000 30.041904 30.009834 30.041904
:
:
: CGMAT cycle number = 37
:
: function value 30.009834
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.99561743E-02
: Gamma decreased to 5.95226660E-02
:
:
: fvalues 0.0000000 30.009834 29.978809 30.009834
:
:
: CGMAT cycle number = 38
:
: function value 29.978809
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.95226660E-02
: Gamma decreased to 5.91285676E-02
:
:
: fvalues 0.0000000 29.978809 29.948734 29.978809
:
:
: CGMAT cycle number = 39
:
: function value 29.948734
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.91285676E-02
: Not converging with gamma equal 5.91285676E-02
: Trying gamma equal 6.10094965E-02
: Gamma decreased to 6.06333092E-02
:
:
: fvalues 0.0000000 29.948734 29.920404 29.948734
:
:
: CGMAT cycle number = 40
:
: function value 29.920404
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:Bond angles : refined atoms 40 2.846 3.000
:Bond angles : others 24 0.650 3.000
:Chiral centres: refined atoms 4 0.028 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 4 0.056 0.200
:VDW; torsion: refined_atoms 12 0.243 0.200
:VDW; torsion.others 12 0.067 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 6.06333092E-02
: Gamma decreased to 6.02913238E-02
:
:
: fvalues 0.0000000 29.920404 29.892975 29.920404
:
:
: CGMAT cycle number = 1
:
: function value 29.892975
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:Bond angles : refined atoms 40 2.844 3.000
:Bond angles : others 24 0.650 3.000
:Chiral centres: refined atoms 4 0.028 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 4 0.056 0.200
:VDW; torsion: refined_atoms 12 0.243 0.200
:VDW; torsion.others 12 0.067 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.0000000
: Not converging with gamma equal 0.0000000
: Trying gamma equal 5.24999984E-02
: Not converging with gamma equal 5.24999984E-02
: Trying gamma equal 0.10762499
: Gamma decreased to 9.65999961E-02
:
:
: fvalues 0.0000000 29.892975 29.877441 29.892975
:
:
: CGMAT cycle number = 2
:
: function value 29.877441
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 9.65999961E-02
: Gamma decreased to 8.65772665E-02
:
:
: fvalues 0.0000000 29.877441 29.860640 29.877441
:
:
: CGMAT cycle number = 3
:
: function value 29.860640
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.65772665E-02
: Gamma decreased to 7.74656981E-02
:
:
: fvalues 0.0000000 29.860640 29.842512 29.860640
:
:
: CGMAT cycle number = 4
:
: function value 29.842512
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.74656981E-02
: Gamma decreased to 6.91824555E-02
:
:
: fvalues 0.0000000 29.842512 29.822935 29.842512
:
:
: CGMAT cycle number = 5
:
: function value 29.822935
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.91824555E-02
: Gamma decreased to 6.16522320E-02
:
:
: fvalues 0.0000000 29.822935 29.801739 29.822935
:
:
: CGMAT cycle number = 6
:
: function value 29.801739
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.16522320E-02
: Gamma decreased to 5.48065752E-02
:
:
: fvalues 0.0000000 29.801739 29.778870 29.801739
:
:
: CGMAT cycle number = 7
:
: function value 29.778870
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.48065752E-02
: Gamma decreased to 4.85832505E-02
:
:
: fvalues 0.0000000 29.778870 29.754221 29.778870
:
:
: CGMAT cycle number = 8
:
: function value 29.754221
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.85832505E-02
: Not converging with gamma equal 4.85832505E-02
: Trying gamma equal 7.82854706E-02
: Gamma decreased to 7.23450258E-02
:
:
: fvalues 0.0000000 29.754221 29.737091 29.754221
:
:
: CGMAT cycle number = 9
:
: function value 29.737091
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.23450258E-02
: Gamma decreased to 6.69446215E-02
:
:
: fvalues 0.0000000 29.737091 29.719170 29.737091
:
:
: CGMAT cycle number = 10
:
: function value 29.719170
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.69446215E-02
: Gamma decreased to 6.20351620E-02
:
:
: fvalues 0.0000000 29.719170 29.700369 29.719170
:
:
: CGMAT cycle number = 11
:
: function value 29.700369
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.20351620E-02
: Gamma decreased to 5.75720184E-02
:
:
: fvalues 0.0000000 29.700369 29.680782 29.700369
:
:
: CGMAT cycle number = 12
:
: function value 29.680782
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.75720184E-02
: Gamma decreased to 5.35146147E-02
:
:
: fvalues 0.0000000 29.680782 29.660429 29.680782
:
:
: CGMAT cycle number = 13
:
: function value 29.660429
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.35146147E-02
: Gamma decreased to 4.98260669E-02
:
:
: fvalues 0.0000000 29.660429 29.639355 29.660429
:
:
: CGMAT cycle number = 14
:
: function value 29.639355
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.98260669E-02
: Not converging with gamma equal 4.98260669E-02
: Trying gamma equal 6.74305037E-02
: Gamma decreased to 6.39096200E-02
:
:
: fvalues 0.0000000 29.639355 29.622938 29.639355
:
:
: CGMAT cycle number = 15
:
: function value 29.622938
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.39096200E-02
: Gamma decreased to 6.07088134E-02
:
:
: fvalues 0.0000000 29.622938 29.606110 29.622938
:
:
: CGMAT cycle number = 16
:
: function value 29.606110
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.07088134E-02
: Gamma decreased to 5.77989891E-02
:
:
: fvalues 0.0000000 29.606110 29.588955 29.606110
:
:
: CGMAT cycle number = 17
:
: function value 29.588955
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.77989891E-02
: Gamma decreased to 5.51536940E-02
:
:
: fvalues 0.0000000 29.588955 29.571524 29.588955
:
:
: CGMAT cycle number = 18
:
: function value 29.571524
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.51536940E-02
: Gamma decreased to 5.27488813E-02
:
:
: fvalues 0.0000000 29.571524 29.553860 29.571524
:
:
: CGMAT cycle number = 19
:
: function value 29.553860
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.27488813E-02
: Gamma decreased to 5.05626872E-02
:
:
: fvalues 0.0000000 29.553860 29.536018 29.553860
:
:
: CGMAT cycle number = 20
:
: function value 29.536018
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.05626872E-02
: Not converging with gamma equal 5.05626872E-02
: Trying gamma equal 6.09967932E-02
: Gamma decreased to 5.89099713E-02
:
:
: fvalues 0.0000000 29.536018 29.520916 29.536018
:
:
: CGMAT cycle number = 21
:
: function value 29.520916
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.89099713E-02
: Gamma decreased to 5.70128597E-02
:
:
: fvalues 0.0000000 29.520916 29.505806 29.520916
:
:
: CGMAT cycle number = 22
:
: function value 29.505806
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.70128597E-02
: Gamma decreased to 5.52882142E-02
:
:
: fvalues 0.0000000 29.505806 29.490562 29.505806
:
:
: CGMAT cycle number = 23
:
: function value 29.490562
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.52882142E-02
: Gamma decreased to 5.37203550E-02
:
:
: fvalues 0.0000000 29.490562 29.475359 29.490562
:
:
: CGMAT cycle number = 24
:
: function value 29.475359
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.37203550E-02
: Gamma decreased to 5.22950292E-02
:
:
: fvalues 0.0000000 29.475359 29.460224 29.475359
:
:
: CGMAT cycle number = 25
:
: function value 29.460224
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.22950292E-02
: Gamma decreased to 5.09992763E-02
:
:
: fvalues 0.0000000 29.460224 29.445110 29.460224
:
:
: CGMAT cycle number = 26
:
: function value 29.445110
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.09992763E-02
: Gamma decreased to 4.98213209E-02
:
:
: fvalues 0.0000000 29.445110 29.430086 29.445110
:
:
: CGMAT cycle number = 27
:
: function value 29.430086
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.98213209E-02
: Gamma decreased to 4.87504527E-02
:
:
: fvalues 0.0000000 29.430086 29.415245 29.430086
:
:
: CGMAT cycle number = 28
:
: function value 29.415245
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.87504527E-02
: Gamma decreased to 4.77769338E-02
:
:
: fvalues 0.0000000 29.415245 29.400536 29.415245
:
:
: CGMAT cycle number = 29
:
: function value 29.400536
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.77769338E-02
: Not converging with gamma equal 4.77769338E-02
: Trying gamma equal 5.24232686E-02
: Gamma decreased to 5.14940023E-02
:
:
: fvalues 0.0000000 29.400536 29.387175 29.400536
:
:
: CGMAT cycle number = 30
:
: function value 29.387175
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.14940023E-02
: Gamma decreased to 5.06492145E-02
:
:
: fvalues 0.0000000 29.387175 29.373995 29.387175
:
:
: CGMAT cycle number = 31
:
: function value 29.373995
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.06492145E-02
: Gamma decreased to 4.98812273E-02
:
:
: fvalues 0.0000000 29.373995 29.360981 29.373995
:
:
: CGMAT cycle number = 32
:
: function value 29.360981
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.98812273E-02
: Gamma decreased to 4.91830558E-02
:
:
: fvalues 0.0000000 29.360981 29.348146 29.360981
:
:
: CGMAT cycle number = 33
:
: function value 29.348146
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.91830558E-02
: Gamma decreased to 4.85483557E-02
:
:
: fvalues 0.0000000 29.348146 29.335510 29.348146
:
:
: CGMAT cycle number = 34
:
: function value 29.335510
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.85483557E-02
: Gamma decreased to 4.79713529E-02
:
:
: fvalues 0.0000000 29.335510 29.323067 29.335510
:
:
: CGMAT cycle number = 35
:
: function value 29.323067
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.79713529E-02
: Gamma decreased to 4.74468060E-02
:
:
: fvalues 0.0000000 29.323067 29.310829 29.323067
:
:
: CGMAT cycle number = 36
:
: function value 29.310829
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.74468060E-02
: Gamma decreased to 4.69699465E-02
:
:
: fvalues 0.0000000 29.310829 29.298843 29.310829
:
:
: CGMAT cycle number = 37
:
: function value 29.298843
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.69699465E-02
: Gamma decreased to 4.65364382E-02
:
:
: fvalues 0.0000000 29.298843 29.287045 29.298843
:
:
: CGMAT cycle number = 38
:
: function value 29.287045
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.65364382E-02
: Gamma decreased to 4.61423397E-02
:
:
: fvalues 0.0000000 29.287045 29.275482 29.287045
:
:
: CGMAT cycle number = 39
:
: function value 29.275482
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.61423397E-02
: Gamma decreased to 4.57840674E-02
:
:
: fvalues 0.0000000 29.275482 29.264126 29.275482
:
:
: CGMAT cycle number = 40
:
: function value 29.264126
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:Bond angles : refined atoms 40 2.783 3.000
:Bond angles : others 24 0.651 3.000
:Chiral centres: refined atoms 4 0.026 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 4 0.057 0.200
:VDW; torsion: refined_atoms 12 0.243 0.200
:VDW; torsion.others 12 0.073 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 4.57840674E-02
: Gamma decreased to 4.54583652E-02
:
:
: fvalues 0.0000000 29.264126 29.253000 29.264126
:
:
: CGMAT cycle number = 1
:
: function value 29.253000
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:Bond angles : refined atoms 40 2.781 3.000
:Bond angles : others 24 0.651 3.000
:Chiral centres: refined atoms 4 0.026 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 4 0.057 0.200
:VDW; torsion: refined_atoms 12 0.243 0.200
:VDW; torsion.others 12 0.073 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.0000000
: Not converging with gamma equal 0.0000000
: Trying gamma equal 5.24999984E-02
: Gamma decreased to 4.19999994E-02
:
:
: fvalues 0.0000000 29.253000 29.243635 29.253000
:
:
: CGMAT cycle number = 2
:
: function value 29.243635
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19999994E-02
: Gamma decreased to 3.24545428E-02
:
:
: fvalues 0.0000000 29.243635 29.232248 29.243635
:
:
: CGMAT cycle number = 3
:
: function value 29.232248
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 3.24545428E-02
: Not converging with gamma equal 3.24545428E-02
: Trying gamma equal 7.80123919E-02
: Gamma decreased to 6.89008236E-02
:
:
: fvalues 0.0000000 29.232248 29.226078 29.232248
:
:
: CGMAT cycle number = 4
:
: function value 29.226078
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.89008236E-02
: Gamma decreased to 6.06175810E-02
:
:
: fvalues 0.0000000 29.226078 29.219261 29.226078
:
:
: CGMAT cycle number = 5
:
: function value 29.219261
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.06175810E-02
: Gamma decreased to 5.30873574E-02
:
:
: fvalues 0.0000000 29.219261 29.211651 29.219261
:
:
: CGMAT cycle number = 6
:
: function value 29.211651
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.30873574E-02
: Gamma decreased to 4.62417006E-02
:
:
: fvalues 0.0000000 29.211651 29.203270 29.211651
:
:
: CGMAT cycle number = 7
:
: function value 29.203270
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.62417006E-02
: Gamma decreased to 4.00183760E-02
:
:
: fvalues 0.0000000 29.203270 29.193890 29.203270
:
:
: CGMAT cycle number = 8
:
: function value 29.193890
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.00183760E-02
: Not converging with gamma equal 4.00183760E-02
: Trying gamma equal 6.97205961E-02
: Gamma decreased to 6.37801513E-02
:
:
: fvalues 0.0000000 29.193890 29.187643 29.193890
:
:
: CGMAT cycle number = 9
:
: function value 29.187643
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.37801513E-02
: Gamma decreased to 5.83797470E-02
:
:
: fvalues 0.0000000 29.187643 29.181007 29.187643
:
:
: CGMAT cycle number = 10
:
: function value 29.181007
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.83797470E-02
: Gamma decreased to 5.34702875E-02
:
:
: fvalues 0.0000000 29.181007 29.173872 29.181007
:
:
: CGMAT cycle number = 11
:
: function value 29.173872
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.34702875E-02
: Gamma decreased to 4.90071438E-02
:
:
: fvalues 0.0000000 29.173872 29.166368 29.173872
:
:
: CGMAT cycle number = 12
:
: function value 29.166368
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.90071438E-02
: Gamma decreased to 4.49497402E-02
:
:
: fvalues 0.0000000 29.166368 29.158276 29.166368
:
:
: CGMAT cycle number = 13
:
: function value 29.158276
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.49497402E-02
: Gamma decreased to 4.12611924E-02
:
:
: fvalues 0.0000000 29.158276 29.149731 29.158276
:
:
: CGMAT cycle number = 14
:
: function value 29.149731
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.12611924E-02
: Not converging with gamma equal 4.12611924E-02
: Trying gamma equal 5.88656291E-02
: Gamma decreased to 5.53447418E-02
:
:
: fvalues 0.0000000 29.149731 29.143272 29.149731
:
:
: CGMAT cycle number = 15
:
: function value 29.143272
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.53447418E-02
: Gamma decreased to 5.21439351E-02
:
:
: fvalues 0.0000000 29.143272 29.136520 29.143272
:
:
: CGMAT cycle number = 16
:
: function value 29.136520
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.21439351E-02
: Gamma decreased to 4.92341109E-02
:
:
: fvalues 0.0000000 29.136520 29.129520 29.136520
:
:
: CGMAT cycle number = 17
:
: function value 29.129520
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.92341109E-02
: Gamma decreased to 4.65888157E-02
:
:
: fvalues 0.0000000 29.129520 29.122269 29.129520
:
:
: CGMAT cycle number = 18
:
: function value 29.122269
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.65888157E-02
: Gamma decreased to 4.41840030E-02
:
:
: fvalues 0.0000000 29.122269 29.114811 29.122269
:
:
: CGMAT cycle number = 19
:
: function value 29.114811
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.41840030E-02
: Gamma decreased to 4.19978090E-02
:
:
: fvalues 0.0000000 29.114811 29.107105 29.114811
:
:
: CGMAT cycle number = 20
:
: function value 29.107105
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19978090E-02
: Gamma decreased to 4.00103591E-02
:
:
: fvalues 0.0000000 29.107105 29.099218 29.107105
:
:
: CGMAT cycle number = 21
:
: function value 29.099218
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.00103591E-02
: Not converging with gamma equal 4.00103591E-02
: Trying gamma equal 4.94959094E-02
: Gamma decreased to 4.75987978E-02
:
:
: fvalues 0.0000000 29.099218 29.092613 29.099218
:
:
: CGMAT cycle number = 22
:
: function value 29.092613
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.75987978E-02
: Gamma decreased to 4.58741523E-02
:
:
: fvalues 0.0000000 29.092613 29.085888 29.092613
:
:
: CGMAT cycle number = 23
:
: function value 29.085888
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.58741523E-02
: Gamma decreased to 4.43062931E-02
:
:
: fvalues 0.0000000 29.085888 29.079048 29.085888
:
:
: CGMAT cycle number = 24
:
: function value 29.079048
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.43062931E-02
: Gamma decreased to 4.28809673E-02
:
:
: fvalues 0.0000000 29.079048 29.072138 29.079048
:
:
: CGMAT cycle number = 25
:
: function value 29.072138
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.28809673E-02
: Gamma decreased to 4.15852144E-02
:
:
: fvalues 0.0000000 29.072138 29.065147 29.072138
:
:
: CGMAT cycle number = 26
:
: function value 29.065147
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.15852144E-02
: Not converging with gamma equal 4.15852144E-02
: Trying gamma equal 4.77694832E-02
: Gamma decreased to 4.65326309E-02
:
:
: fvalues 0.0000000 29.065147 29.058941 29.065147
:
:
: CGMAT cycle number = 27
:
: function value 29.058941
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.65326309E-02
: Gamma decreased to 4.54082191E-02
:
:
: fvalues 0.0000000 29.058941 29.052719 29.058941
:
:
: CGMAT cycle number = 28
:
: function value 29.052719
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.54082191E-02
: Gamma decreased to 4.43860255E-02
:
:
: fvalues 0.0000000 29.052719 29.046501 29.052719
:
:
: CGMAT cycle number = 29
:
: function value 29.046501
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.43860255E-02
: Gamma decreased to 4.34567593E-02
:
:
: fvalues 0.0000000 29.046501 29.040226 29.046501
:
:
: CGMAT cycle number = 30
:
: function value 29.040226
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.34567593E-02
: Gamma decreased to 4.26119715E-02
:
:
: fvalues 0.0000000 29.040226 29.033924 29.040226
:
:
: CGMAT cycle number = 31
:
: function value 29.033924
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.26119715E-02
: Not converging with gamma equal 4.26119715E-02
: Trying gamma equal 4.66439128E-02
: Gamma decreased to 4.58375253E-02
:
:
: fvalues 0.0000000 29.033924 29.028139 29.033924
:
:
: CGMAT cycle number = 32
:
: function value 29.028139
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.58375253E-02
: Gamma decreased to 4.51044440E-02
:
:
: fvalues 0.0000000 29.028139 29.022421 29.028139
:
:
: CGMAT cycle number = 33
:
: function value 29.022421
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.51044440E-02
: Gamma decreased to 4.44380082E-02
:
:
: fvalues 0.0000000 29.022421 29.016649 29.022421
:
:
: CGMAT cycle number = 34
:
: function value 29.016649
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.44380082E-02
: Gamma decreased to 4.38321568E-02
:
:
: fvalues 0.0000000 29.016649 29.010910 29.016649
:
:
: CGMAT cycle number = 35
:
: function value 29.010910
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.38321568E-02
: Gamma decreased to 4.32813838E-02
:
:
: fvalues 0.0000000 29.010910 29.005224 29.010910
:
:
: CGMAT cycle number = 36
:
: function value 29.005224
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.32813838E-02
: Gamma decreased to 4.27806787E-02
:
:
: fvalues 0.0000000 29.005224 28.999550 29.005224
:
:
: CGMAT cycle number = 37
:
: function value 28.999550
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.27806787E-02
: Gamma decreased to 4.23254929E-02
:
:
: fvalues 0.0000000 28.999550 28.993898 28.999550
:
:
: CGMAT cycle number = 38
:
: function value 28.993898
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.23254929E-02
: Not converging with gamma equal 4.23254929E-02
: Trying gamma equal 4.44979668E-02
: Gamma decreased to 4.40634713E-02
:
:
: fvalues 0.0000000 28.993898 28.988565 28.993898
:
:
: CGMAT cycle number = 39
:
: function value 28.988565
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.40634713E-02
: Gamma decreased to 4.36684750E-02
:
:
: fvalues 0.0000000 28.988565 28.983236 28.988565
:
:
: CGMAT cycle number = 40
:
: function value 28.983236
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:Bond angles : refined atoms 40 2.754 3.000
:Bond angles : others 24 0.651 3.000
:Chiral centres: refined atoms 4 0.025 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.081 0.200
:VDW; torsion: refined_atoms 12 0.243 0.200
:VDW; torsion.others 12 0.075 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 4.36684750E-02
: Gamma decreased to 4.33093868E-02
:
:
: fvalues 0.0000000 28.983236 28.977982 28.983236
:
: **** Final optimisation stage ****
:
:
:
: CGMAT cycle number = 1
:
: function value 28.977982
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:Bond angles : refined atoms 40 2.753 3.000
:Bond angles : others 24 0.651 3.000
:Chiral centres: refined atoms 4 0.025 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.081 0.200
:VDW; torsion: refined_atoms 12 0.243 0.200
:VDW; torsion.others 12 0.076 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.0000000
: Not converging with gamma equal 0.0000000
: Trying gamma equal 5.24999984E-02
: Gamma decreased to 4.19999994E-02
:
:
: fvalues 0.0000000 28.977982 28.973661 28.977982
:
:
: CGMAT cycle number = 2
:
: function value 28.973661
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19999994E-02
: Gamma decreased to 3.24545428E-02
:
:
: fvalues 0.0000000 28.973661 28.968380 28.973661
:
:
: CGMAT cycle number = 3
:
: function value 28.968380
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 3.24545428E-02
: Not converging with gamma equal 3.24545428E-02
: Trying gamma equal 7.80123919E-02
: Gamma decreased to 6.89008236E-02
:
:
: fvalues 0.0000000 28.968380 28.965488 28.968380
:
:
: CGMAT cycle number = 4
:
: function value 28.965488
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.89008236E-02
: Gamma decreased to 6.06175810E-02
:
:
: fvalues 0.0000000 28.965488 28.962254 28.965488
:
:
: CGMAT cycle number = 5
:
: function value 28.962254
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.06175810E-02
: Gamma decreased to 5.30873574E-02
:
:
: fvalues 0.0000000 28.962254 28.958670 28.962254
:
:
: CGMAT cycle number = 6
:
: function value 28.958670
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.30873574E-02
: Gamma decreased to 4.62417006E-02
:
:
: fvalues 0.0000000 28.958670 28.954634 28.958670
:
:
: CGMAT cycle number = 7
:
: function value 28.954634
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.62417006E-02
: Gamma decreased to 4.00183760E-02
:
:
: fvalues 0.0000000 28.954634 28.950089 28.954634
:
:
: CGMAT cycle number = 8
:
: function value 28.950089
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.00183760E-02
: Not converging with gamma equal 4.00183760E-02
: Trying gamma equal 6.97205961E-02
: Gamma decreased to 6.37801513E-02
:
:
: fvalues 0.0000000 28.950089 28.947037 28.950089
:
:
: CGMAT cycle number = 9
:
: function value 28.947037
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.37801513E-02
: Gamma decreased to 5.83797470E-02
:
:
: fvalues 0.0000000 28.947037 28.943735 28.947037
:
:
: CGMAT cycle number = 10
:
: function value 28.943735
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.83797470E-02
: Gamma decreased to 5.34702875E-02
:
:
: fvalues 0.0000000 28.943735 28.940212 28.943735
:
:
: CGMAT cycle number = 11
:
: function value 28.940212
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.34702875E-02
: Gamma decreased to 4.90071438E-02
:
:
: fvalues 0.0000000 28.940212 28.936430 28.940212
:
:
: CGMAT cycle number = 12
:
: function value 28.936430
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.90071438E-02
: Gamma decreased to 4.49497402E-02
:
:
: fvalues 0.0000000 28.936430 28.932369 28.936430
:
:
: CGMAT cycle number = 13
:
: function value 28.932369
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.49497402E-02
: Gamma decreased to 4.12611924E-02
:
:
: fvalues 0.0000000 28.932369 28.928024 28.932369
:
:
: CGMAT cycle number = 14
:
: function value 28.928024
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.12611924E-02
: Not converging with gamma equal 4.12611924E-02
: Trying gamma equal 5.88656291E-02
: Gamma decreased to 5.53447418E-02
:
:
: fvalues 0.0000000 28.928024 28.924654 28.928024
:
:
: CGMAT cycle number = 15
:
: function value 28.924654
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.53447418E-02
: Gamma decreased to 5.21439351E-02
:
:
: fvalues 0.0000000 28.924654 28.921169 28.924654
:
:
: CGMAT cycle number = 16
:
: function value 28.921169
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.21439351E-02
: Gamma decreased to 4.92341109E-02
:
:
: fvalues 0.0000000 28.921169 28.917494 28.921169
:
:
: CGMAT cycle number = 17
:
: function value 28.917494
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.92341109E-02
: Gamma decreased to 4.65888157E-02
:
:
: fvalues 0.0000000 28.917494 28.913664 28.917494
:
:
: CGMAT cycle number = 18
:
: function value 28.913664
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.65888157E-02
: Gamma decreased to 4.41840030E-02
:
:
: fvalues 0.0000000 28.913664 28.909664 28.913664
:
:
: CGMAT cycle number = 19
:
: function value 28.909664
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.41840030E-02
: Gamma decreased to 4.19978090E-02
:
:
: fvalues 0.0000000 28.909664 28.905521 28.909664
:
:
: CGMAT cycle number = 20
:
: function value 28.905521
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19978090E-02
: Not converging with gamma equal 4.19978090E-02
: Trying gamma equal 5.24319150E-02
: Gamma decreased to 5.03450930E-02
:
:
: fvalues 0.0000000 28.905521 28.902020 28.905521
:
:
: CGMAT cycle number = 21
:
: function value 28.902020
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.03450930E-02
: Gamma decreased to 4.84479815E-02
:
:
: fvalues 0.0000000 28.902020 28.898426 28.902020
:
:
: CGMAT cycle number = 22
:
: function value 28.898426
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.84479815E-02
: Gamma decreased to 4.67233360E-02
:
:
: fvalues 0.0000000 28.898426 28.894768 28.898426
:
:
: CGMAT cycle number = 23
:
: function value 28.894768
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.67233360E-02
: Gamma decreased to 4.51554768E-02
:
:
: fvalues 0.0000000 28.894768 28.891022 28.894768
:
:
: CGMAT cycle number = 24
:
: function value 28.891022
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.51554768E-02
: Not converging with gamma equal 4.51554768E-02
: Trying gamma equal 5.26384413E-02
: Gamma decreased to 5.11418469E-02
:
:
: fvalues 0.0000000 28.891022 28.887703 28.891022
:
:
: CGMAT cycle number = 25
:
: function value 28.887703
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.11418469E-02
: Gamma decreased to 4.97813076E-02
:
:
: fvalues 0.0000000 28.887703 28.884359 28.887703
:
:
: CGMAT cycle number = 26
:
: function value 28.884359
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.97813076E-02
: Gamma decreased to 4.85444553E-02
:
:
: fvalues 0.0000000 28.884359 28.880930 28.884359
:
:
: CGMAT cycle number = 27
:
: function value 28.880930
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.85444553E-02
: Gamma decreased to 4.74200435E-02
:
:
: fvalues 0.0000000 28.880930 28.877552 28.880930
:
:
: CGMAT cycle number = 28
:
: function value 28.877552
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.74200435E-02
: Gamma decreased to 4.63978499E-02
:
:
: fvalues 0.0000000 28.877552 28.874088 28.877552
:
:
: CGMAT cycle number = 29
:
: function value 28.874088
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.63978499E-02
: Not converging with gamma equal 4.63978499E-02
: Trying gamma equal 5.12764975E-02
: Gamma decreased to 5.03007695E-02
:
:
: fvalues 0.0000000 28.874088 28.870937 28.874088
:
:
: CGMAT cycle number = 30
:
: function value 28.870937
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.03007695E-02
: Gamma decreased to 4.94137406E-02
:
:
: fvalues 0.0000000 28.870937 28.867744 28.870937
:
:
: CGMAT cycle number = 31
:
: function value 28.867744
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.94137406E-02
: Gamma decreased to 4.86073531E-02
:
:
: fvalues 0.0000000 28.867744 28.864532 28.867744
:
:
: CGMAT cycle number = 32
:
: function value 28.864532
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.86073531E-02
: Gamma decreased to 4.78742719E-02
:
:
: fvalues 0.0000000 28.864532 28.861330 28.864532
:
:
: CGMAT cycle number = 33
:
: function value 28.861330
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.78742719E-02
: Gamma decreased to 4.72078361E-02
:
:
: fvalues 0.0000000 28.861330 28.858130 28.861330
:
:
: CGMAT cycle number = 34
:
: function value 28.858130
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.72078361E-02
: Not converging with gamma equal 4.72078361E-02
: Trying gamma equal 5.03885560E-02
: Gamma decreased to 4.97524105E-02
:
:
: fvalues 0.0000000 28.858130 28.855083 28.858130
:
:
: CGMAT cycle number = 35
:
: function value 28.855083
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.97524105E-02
: Gamma decreased to 4.91740964E-02
:
:
: fvalues 0.0000000 28.855083 28.852051 28.855083
:
:
: CGMAT cycle number = 36
:
: function value 28.852051
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.91740964E-02
: Gamma decreased to 4.86483574E-02
:
:
: fvalues 0.0000000 28.852051 28.849003 28.852051
:
:
: CGMAT cycle number = 37
:
: function value 28.849003
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.86483574E-02
: Gamma decreased to 4.81704138E-02
:
:
: fvalues 0.0000000 28.849003 28.845972 28.849003
:
:
: CGMAT cycle number = 38
:
: function value 28.845972
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.81704138E-02
: Not converging with gamma equal 4.81704138E-02
: Trying gamma equal 5.04515134E-02
: Gamma decreased to 4.99952920E-02
:
:
: fvalues 0.0000000 28.845972 28.843063 28.845972
:
:
: CGMAT cycle number = 39
:
: function value 28.843063
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.99952920E-02
: Gamma decreased to 4.95805480E-02
:
:
: fvalues 0.0000000 28.843063 28.840176 28.843063
:
:
: CGMAT cycle number = 40
:
: function value 28.840176
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 10 0.000 0.020
:Bond angles : refined atoms 40 2.740 3.000
:Bond angles : others 24 0.651 3.000
:Chiral centres: refined atoms 4 0.024 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.081 0.200
:VDW; torsion: refined_atoms 14 0.225 0.200
:VDW; torsion.others 12 0.077 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 4.95805480E-02
: Gamma decreased to 4.92035076E-02
:
:
: fvalues 0.0000000 28.840176 28.837288 28.840176
: chir_max = 4.13386822E-02
: rms = 0.35088748
: angle = 0.91783828
: Time in seconds: CPU = 0.50
: Elapsed = 0.00
:
: **** Things for loggraph, R factor and others vs cycle ****
:
:
:$TABLE: Rfactor analysis, stats vs cycle :
:$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
::FOM vs cycle :N:1,4:
::-LL vs cycle :N:1,5:
::-LLfree vs cycle :N:1,6:
::Geometry vs cycle:N:1,7,8,9,10,11:
:$$
: Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$
:$$
: 0 0.0 0.0 0.0 0. 0.0 0.0304 1.521 4.292 1.431 0.186
: 1 0.0 0.0 0.0 0. 0.0 0.0097 0.483 3.122 1.041 0.030
: 2 0.0 0.0 0.0 0. 0.0 0.0072 0.358 3.050 1.017 0.030
: 3 0.0 0.0 0.0 0. 0.0 0.0071 0.356 3.020 1.007 0.032
: 4 0.0 0.0 0.0 0. 0.0 0.0071 0.356 2.995 0.998 0.033
: 5 0.0 0.0 0.0 0. 0.0 0.0071 0.355 2.985 0.995 0.032
: 6 0.0 0.0 0.0 0. 0.0 0.0071 0.355 2.981 0.994 0.032
: 7 0.0 0.0 0.0 0. 0.0 0.0071 0.355 2.976 0.992 0.032
: 8 0.0 0.0 0.0 0. 0.0 0.0071 0.355 2.971 0.990 0.032
: 9 0.0 0.0 0.0 0. 0.0 0.0071 0.355 2.967 0.989 0.032
: 10 0.0 0.0 0.0 0. 0.0 0.0071 0.355 2.962 0.987 0.032
: 11 0.0 0.0 0.0 0. 0.0 0.0071 0.355 2.957 0.986 0.032
: 12 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.951 0.984 0.032
: 13 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.946 0.982 0.032
: 14 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.941 0.980 0.031
: 15 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.935 0.978 0.031
: 16 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.930 0.977 0.031
: 17 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.926 0.975 0.031
: 18 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.921 0.974 0.031
: 19 0.0 0.0 0.0 0. 0.0 0.0071 0.354 2.917 0.972 0.031
: 20 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.912 0.971 0.030
: 21 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.908 0.969 0.030
: 22 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.903 0.968 0.030
: 23 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.899 0.966 0.030
: 24 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.895 0.965 0.030
: 25 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.891 0.964 0.030
: 26 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.888 0.963 0.030
: 27 0.0 0.0 0.0 0. 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/3/3GP.cif
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_06:06:09_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_06:06:09_2015_modification_1.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb
PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 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: /lmb/home/pemsley/data/greg-data/test-LIG.pdb
PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 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: /lmb/home/pemsley/data/greg-data/test-LIG.pdb
PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 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 /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LIG.cif
INFO:: comp-id: LIG is marked for non-autoloading - stopping now
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_06:06:09_2015_modification_2.pdb.gz
No graphics! Can't make Map Selection dialog.
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 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: /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
PDB file /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 0/113
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 0/117
INFO:: fill_ghost_info Constructed 6 ghosts
Ghost 0 name: "NCS found from matching Chain C onto Chain A"
Ghost 1 name: "NCS found from matching Chain E onto Chain A"
Ghost 2 name: "NCS found from matching Chain G onto Chain A"
Ghost 3 name: "NCS found from matching Chain D onto Chain B"
Ghost 4 name: "NCS found from matching Chain F onto Chain B"
Ghost 5 name: "NCS found from matching Chain H onto Chain B"
Molecule 109 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.144 seconds to read MTZ file
INFO:: 0.086 seconds to initialize map
INFO:: 0.062 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:: 0.007 seconds for contour map
INFO:: 0.312 seconds in total
INFO:: making difference map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.074 seconds to read MTZ file
INFO:: 0.002 seconds to initialize map
INFO:: 0.06 seconds for FFT
INFO:: 0.011 seconds for statistics
Map mean: ........ 2.094e-06
Map sigma: ....... 0.03339
Map maximum: ..... 0.3661
Map minimum: ..... -0.1917
INFO:: 0.003 seconds for contour map
INFO:: 0.15 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 102890
-0.02498 142998
0.01126 471775
0.0475 106846
0.08375 56087
0.12 21597
0.1562 6911
0.1925 2135
0.2287 920
0.265 467
0.3012 346
0.3374 216
0.3737 118
0.4099 117
0.4462 80
0.4824 50
0.5186 28
0.5549 33
0.5911 15
0.6274 14
0.6636 11
0.6998 2
0.7361 7
0.7723 0
INFO:: find_clusters map_rms is 0.1711
INFO:: Using density cut-off: 0.1711 (1 sigma) (mean -0.02168 stdev: 0.08862)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
debug:: n_ligands_for_cluster() top_score 4.042 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.007 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.092 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.857 and 3 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.387 and 4 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.611 and 4 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.1 and 2 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.691 and 2 are decent out of 12
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.123 and 2 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.841 and 5 are decent out of 12
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 136 read successfully
DEBUG:: there were 0 types with no dictionary
Symmetry available for this molecule
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Sun_Sep__6_06:06:17_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_06:06:17_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_06:06:17_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_06:06:17_2015_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/dipole-residues.pdb
PDB file /lmb/home/pemsley/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 138 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING: in init_refmac_mon_lib file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 139 read successfully
DEBUG:: there were 0 types with no dictionary
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 139
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 139
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb
PDB file /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 140 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.025 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.014 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.069e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.015 seconds for contour map
INFO:: 0.056 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 140
Sequence: ?EYTVITPGARTR
Confidence: 1
From : HEYTVITPGARTR
Chain id: 0 Offset: 53
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Sun_Sep__6_06:06:19_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_06:06:20_2015_modification_0.pdb.gz
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: Matching/moving molecule number 144 to 144
ERROR:: No symmetry available
INFO:: LSQ matched 125 atoms
INFO:: 125 matched atoms had:
mean devi: 0.1419
rms devi: 0.1486
max devi: 0.2431
min devi: 0.02832
INFO:: Axis orientation: ( 0.3864, -0.6781, -0.6252)
INFO:: Rotation in CCP4 Polar Angles: Polar = (128.694,-60.3228,0.295209)
INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Sun_Sep__6_06:06:20_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: /lmb/home/pemsley/data/greg-data/1wly.pdb
PDB file /lmb/home/pemsley/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 145 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1yb5.pdb
PDB file /lmb/home/pemsley/data/greg-data/1yb5.pdb has been read.
Spacegroup: P 21 21 2
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 324/324
INFO:: NCS chain comparison 0/324
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 146 read successfully
DEBUG:: there were 2 types with no dictionary
INFO:: using standard CCP4 Refmac dictionary to search for "CL"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CL.cif
INFO:: using standard CCP4 Refmac dictionary to search for "NAP"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/n/NAP.cif
INFO:: reference 145 has 750 atoms selected
INFO:: moving 146 has 842 atoms selected
superposing...
number of Ca atoms in selections: 110 (moving) and 100 (reference)
Another Go...
Moving Reference Distance(/A)
A 6
A 7
A 8 <---> A 2 : 0.7510
A 9 <---> A 3 : 0.9422
A 10 <---> A 4 : 0.6300
A 11 <---> A 5 : 0.7119
A 12 <---> A 6 : 0.6310
A 13 <---> A 7 : 0.4675
A 14 <---> A 8 : 0.4264
A 15 <---> A 9 : 0.9792
A 16 <---> A 10 : 0.7549
A 17 <---> A 11 : 0.4884
A 18 <---> A 12 : 0.7451
A 19 <---> A 13 : 0.4606
A 20 <---> A 14 : 1.2809
A 21 <---> A 15 : 1.2412
A 22 <---> A 16 : 1.0733
A 23 <---> A 17 : 0.9730
A 24 <---> A 18 : 0.4705
A 25 <---> A 19 : 0.3560
A 26 <---> A 20 : 3.1145
A 27
A 28 <---> A 21 : 1.5754
A 29 <---> A 22 : 1.6322
A 30
A 31 <---> A 23 : 1.9973
A 32 <---> A 25 : 1.8324
A 33 <---> A 26 : 0.9310
A 34 <---> A 27 : 0.6808
A 35 <---> A 28 : 0.2674
A 36 <---> A 29 : 0.5995
A 37 <---> A 30 : 0.6992
A 38 <---> A 31 : 0.8620
A 39 <---> A 32 : 0.8421
A 40 <---> A 33 : 0.7208
A 41 <---> A 34 : 0.8681
A 42 <---> A 35 : 0.7781
A 43 <---> A 36 : 0.6211
A 44 <---> A 37 : 0.4657
A 45 <---> A 38 : 0.7475
A 46 <---> A 39 : 0.5170
A 47 <---> A 40 : 0.5058
A 48 <---> A 41 : 0.8897
A 49 <---> A 42 : 0.5835
A 50 <---> A 43 : 0.4347
A 51 <---> A 44 : 0.6192
A 52 <---> A 45 : 0.2150
A 53 <---> A 46 : 0.7474
A 54 <---> A 47 : 1.0213
A 55 <---> A 48 : 0.9208
A 56 <---> A 49 : 0.9392
A 57
A 58
A 59
A 60
A 61
A 62
A 63
A 64
A 65 <---> A 60 : 0.4666
A 66 <---> A 61 : 0.0523
A 67 <---> A 62 : 1.0719
A 68 <---> A 63 : 0.7933
A 69 <---> A 64 : 0.8916
A 70 <---> A 65 : 1.2580
A 71 <---> A 66 : 0.6932
A 72 <---> A 67 : 1.0345
A 73 <---> A 68 : 1.4417
A 74 <---> A 69 : 0.9092
A 75 <---> A 70 : 1.6166
A 76 <---> A 71 : 0.8741
A 77 <---> A 72 : 0.2388
A 78 <---> A 73 : 0.3118
A 79 <---> A 74 : 0.3887
A 80 <---> A 75 : 0.7613
A 81 <---> A 76 : 0.9044
A 82 <---> A 77 : 0.6090
A 83 <---> A 78 : 1.7978
A 84 <---> A 79 : 1.9256
A 85 <---> A 80 : 1.3416
A 86 <---> A 81 : 0.5658
A 87 <---> A 82 : 0.4480
A 88 <---> A 83 : 0.9078
A 89 <---> A 84 : 0.3625
A 90 <---> A 85 : 0.4040
A 91 <---> A 86 : 0.4586
A 92 <---> A 87 : 0.4340
A 93 <---> A 88 : 0.3664
A 94 <---> A 89 : 0.4921
A 95 <---> A 90 : 0.6498
A 96 <---> A 91 : 1.5805
A 97 <---> A 92 : 2.8839
A 98
A 99
A 100
Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG
Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA
Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY
Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_1yb5.pdb_Sun_Sep__6_06:06:21_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 /lmb/home/pemsley/data/greg-data/1pyd.pdb
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2qd9.pdb
PDB file /lmb/home/pemsley/data/greg-data/2qd9.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 147 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: using standard CCP4 Refmac dictionary to search for "LGF"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LGF.cif
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2gtn.pdb
PDB file /lmb/home/pemsley/data/greg-data/2gtn.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 0/337
Molecule 148 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: using standard CCP4 Refmac dictionary to search for "LIE"
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LIE.cif
INFO:: reference 147 has 169 atoms selected
INFO:: moving 148 has 169 atoms selected
superposing...
number of Ca atoms in selections: 21 (moving) and 21 (reference)
Another Go...
Moving Reference Distance(/A)
A 140 <---> A 140 : 0.1804
A 141 <---> A 141 : 0.0760
A 142 <---> A 142 : 0.1052
A 143 <---> A 143 : 0.1246
A 144 <---> A 144 : 0.1370
A 145 <---> A 145 : 0.1380
A 146 <---> A 146 : 0.1662
A 147 <---> A 147 : 0.2744
A 148 <---> A 148 : 0.2728
A 149 <---> A 149 : 0.1173
A 150 <---> A 150 : 0.1684
A 151 <---> A 151 : 0.0928
A 152 <---> A 152 : 0.1200
A 153 <---> A 153 : 0.1281
A 154 <---> A 154 : 0.2539
A 155 <---> A 155 : 0.6351
A 156 <---> A 156 : 0.1300
A 157 <---> A 157 : 0.1478
A 158 <---> A 158 : 0.2238
A 159 <---> A 159 : 0.2271
A 160 <---> A 160 : 0.2372
Moving: YIHSADIIHRDLKPSNLAVNE
Target: YIHSADIIHRDLKPSNLAVNE
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2gtn.pdb_Sun_Sep__6_06:06:22_2015_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix:
| 0.9998, 0.009845, -0.01938|
| -0.009814, 1, 0.001689|
| 0.0194, -0.001498, 0.9998|
( 0.3207, 0.6598, 0.8819)
Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491
Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832
Translation - Angstroms 0.3207 0.6598 0.8819
INFO: core rmsd achieved: 0.2210 Angstroems
number of residues in reference structure: 330
number of residues in moving structure: 337
number of residues in aligned sections (reference): 21
number of residues in aligned sections (moving): 21
number of aligned residues: 21
number of gaps: 0
number of misdirections: 0
number of SSE combinations: 1.0000
sequence identity: 100.0000%
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O S
INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000
READ-INS:: Spacegroup: "I 21 3"
INFO:: chain has 121 residues
Symmetry available for this molecule
Molecule 149 read successfully
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0290 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0160 seconds for FFT
INFO:: 0.0030 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 2.9776
Map minimum: ..... -0.8750
INFO:: 0.0190 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 2
2.3885 0
INFO:: installing ghost map with name :Map 150 NCS found from matching Chain B onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
| 0.9637, -0.07462, -0.2563|
| 0.2651, 0.3804, 0.886|
| 0.0314, -0.9218, 0.3864|
( 38.09, -17.87, 14.32)
inverse of reference matcher transformation:
| 0.9637, 0.2651, 0.0314|
| -0.07462, 0.3804, -0.9218|
| -0.2563, 0.886, 0.3864|
( -32.42, 22.84, 20.06)
boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985)
INFO:: There were 2.0000 maps contributing to the average
INFO:: rescaling by 0.5000
INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: 0.0004 st.d: 0.3236
Map statistics: min: -1.4496, max: 2.3411
-1.4022 3
-1.3074 1
-1.2127 4
-1.1179 8
-1.0231 5
-0.9283 32
-0.8336 104
-0.7388 349
-0.6440 1163
-0.5493 3433
-0.4545 8783
-0.3597 17620
-0.2650 27133
-0.1702 32345
-0.0754 31462
0.0193 26827
0.1141 20587
0.2089 15419
0.3036 11965
0.3984 8787
0.4932 6637
0.5879 4777
0.6827 3343
0.7775 2426
0.8722 1733
0.9670 1142
1.0618 796
1.1565 469
1.2513 296
1.3461 188
1.4409 96
1.5356 80
1.6304 34
1.7252 20
1.8199 14
1.9147 6
2.0095 4
2.1042 3
2.1990 0
2.2938 2
2.3885 0
no diffs
NCS target chain has 93 peers.
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 155 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:23_2015_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:23_2015_modification_1.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:23_2015_modification_2.pdb.gz
%%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe()
INFO:: NCS chain comparison 90/93
First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100
INFO:: LSQ matched 90 atoms
INFO:: 90 matched atoms had:
mean devi: 0.3643
rms devi: 0.4571
max devi: 2.1351
min devi: 0.0881
find_ncs_matrix returns (LSQ)
| 0.9705, -0.04634, -0.2366|
| 0.2357, 0.3884, 0.8908|
| 0.05061, -0.9203, 0.3878|
( 37.8, -17.18, 13.82)
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 155 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 155 and ichain: 0
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 0
Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 90/93
First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100
INFO:: LSQ matched 90 atoms
INFO:: 90 matched atoms had:
mean devi: 0.3643
rms devi: 0.4571
max devi: 2.1351
min devi: 0.0881
find_ncs_matrix returns (LSQ)
| 0.9705, -0.04634, -0.2366|
| 0.2357, 0.3884, 0.8908|
| 0.05061, -0.9203, 0.3878|
( 37.8, -17.18, 13.82)
Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:23_2015_modification_3.pdb.gz
INFO:: mutate 2 A to a TRP
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:23_2015_modification_4.pdb.gz
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 155 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 155 and ichain: 0
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 0
Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 92/93
First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700
INFO:: LSQ matched 93 atoms
INFO:: 93 matched atoms had:
mean devi: 0.3427
rms devi: 0.4454
max devi: 2.1352
min devi: 0.0124
find_ncs_matrix returns (LSQ)
| 0.9705, -0.04643, -0.2365|
| 0.2356, 0.3891, 0.8906|
| 0.05068, -0.92, 0.3886|
( 37.8, -17.17, 13.81)
Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Sun_Sep__6_06:06:23_2015_modification_5.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1t6q.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb1t6q.ent has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 110/110
INFO:: NCS chain comparison 110/110
INFO:: fill_ghost_info Constructed 2 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Molecule 156 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: mutate 50 A to a ASP
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Sun_Sep__6_06:06:24_2015_modification_0.pdb.gz
%%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe()
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2048
rms devi: 0.2651
max devi: 1.1707
min devi: 0.0160
find_ncs_matrix returns (LSQ)
| 0.5407, 0.4775, 0.6926|
| -0.4862, -0.4944, 0.7205|
| 0.6865, -0.7263, -0.03511|
( -28.15, 65.89, 42.9)
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2275
rms devi: 0.3035
max devi: 1.6549
min devi: 0.0661
find_ncs_matrix returns (LSQ)
| 0.5303, -0.4851, 0.6953|
| 0.4758, -0.5085, -0.7177|
| 0.7017, 0.7114, -0.03884|
( 18.19, 77.78, -25.69)
INFO:: fill_ghost_info Constructed 2 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 156 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 156 and ichain: 0
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 0
Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2048
rms devi: 0.2651
max devi: 1.1707
min devi: 0.0160
find_ncs_matrix returns (LSQ)
| 0.5407, 0.4775, 0.6926|
| -0.4862, -0.4944, 0.7205|
| 0.6865, -0.7263, -0.03511|
( -28.15, 65.89, 42.9)
Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2275
rms devi: 0.3035
max devi: 1.6549
min devi: 0.0661
find_ncs_matrix returns (LSQ)
| 0.5303, -0.4851, 0.6953|
| 0.4758, -0.5085, -0.7177|
| 0.7017, 0.7114, -0.03884|
( 18.19, 77.78, -25.69)
Adding ghost with name: NCS found from matching Chain C onto Chain A
INFO:: set_ncs_master_chain Constructed 2 ghosts
Ghost info:: NCS found from matching Chain B onto Chain A
Ghost info:: NCS found from matching Chain C onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Sun_Sep__6_06:06:24_2015_modification_1.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Sun_Sep__6_06:06:24_2015_modification_2.pdb.gz
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
INFO:: fill_ghost_info Constructed 3 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 157 read successfully
DEBUG:: there were 0 types with no dictionary
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 157 and chain_id: B
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 1
Checking chains for NCS matching to chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 540 in second selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had:
mean devi: 2.4989
rms devi: 2.7962
max devi: 6.6860
min devi: 0.4401
find_ncs_matrix returns (LSQ)
| 0.7026, 0.1278, 0.7|
| 0.6024, 0.4169, -0.6807|
| -0.3788, 0.8999, 0.2159|
( 62.25, -87.53, -9.128)
Adding ghost with name: NCS found from matching Chain A onto Chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had:
mean devi: 2.6728
rms devi: 2.9369
max devi: 6.1200
min devi: 0.2483
find_ncs_matrix returns (LSQ)
| -0.3504, -0.8022, -0.4834|
| -0.7587, -0.05952, 0.6488|
| -0.5492, 0.594, -0.5878|
( -29.05, 14.61, -72.53)
Adding ghost with name: NCS found from matching Chain C onto Chain B
INFO:: NCS chain comparison 61/62
First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had:
mean devi: 1.7317
rms devi: 1.9769
max devi: 7.9453
min devi: 0.5297
find_ncs_matrix returns (LSQ)
| -0.3815, -0.9208, -0.08098|
| -0.9191, 0.3685, 0.1396|
| -0.09874, 0.1277, -0.9869|
( -11.18, 4.757, -127.2)
Adding ghost with name: NCS found from matching Chain D onto Chain B
INFO:: NCS chain comparison 0/62
INFO:: set_ncs_master_chain Constructed 3 ghosts
Ghost info:: NCS found from matching Chain A onto Chain B
Ghost info:: NCS found from matching Chain C onto Chain B
Ghost info:: NCS found from matching Chain D onto Chain B
Symmetry available for this molecule
INFO:: Matching/moving molecule number 158 to 157
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had:
mean devi: 0.2239
rms devi: 0.2350
max devi: 0.3369
min devi: 0.0588
INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925)
INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Sun_Sep__6_06:06:26_2015_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix:
| 0.3395, 0.5177, 0.7853|
| 0.8624, 0.162, -0.4796|
| -0.3755, 0.8401, -0.3915|
( 90.55, -91.12, -47.52)
INFO:: fractional coordinates matrix:
| 0.8374, 0.1106, 0.6656|
| 0.9958, -0.3359, -0.7249|
| -0.2868, 0.6992, -0.3915|
( 0.4296, -1.191, -0.411)
Symmetry available for this molecule
INFO:: Matching/moving molecule number 159 to 157
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had:
mean devi: 0.1943
rms devi: 0.2112
max devi: 0.3583
min devi: 0.0329
INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095)
INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Sun_Sep__6_06:06:26_2015_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix:
| -0.6203, -0.2279, -0.7505|
| -0.4559, -0.6739, 0.5814|
| -0.6382, 0.7028, 0.3141|
( -22.14, -19.93, 1.626)
INFO:: fractional coordinates matrix:
| -0.8835, -0.09252, -0.543|
| -0.5264, -0.4107, 0.8789|
| -0.4875, 0.7087, 0.3141|
( -0.381, -0.2605, 0.01406)
Symmetry available for this molecule
INFO:: Matching/moving molecule number 160 to 157
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had:
mean devi: 0.4174
rms devi: 0.4531
max devi: 0.7926
min devi: 0.0759
INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411)
INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Sun_Sep__6_06:06:26_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: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
INFO:: fill_ghost_info Constructed 3 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 161 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz
Number of OBSERVED reflections: 20903
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 112, 112, 150)
INFO:: 0.0370 seconds to read MTZ file
INFO:: 0.0200 seconds to initialize map
INFO:: 0.0230 seconds for FFT
INFO:: 0.0040 seconds for statistics
Map mean: ........ -0.0000
Map sigma: ....... 0.2241
Map maximum: ..... 1.7219
Map minimum: ..... -0.8818
INFO:: 0.0080 seconds for contour map
INFO:: 0.0920 seconds in total
INFO:: NCS chain comparison 62/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had:
mean devi: 2.4989
rms devi: 2.7962
max devi: 6.6860
min devi: 0.4401
find_ncs_matrix returns (LSQ)
| 0.7026, 0.6024, -0.3788|
| 0.1278, 0.4169, 0.8999|
| 0.7, -0.6807, 0.2159|
( 5.528, 36.75, -101.2)
INFO:: NCS chain comparison 66/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 66 atoms
INFO:: 66 matched atoms had:
mean devi: 1.9713
rms devi: 2.1729
max devi: 4.5411
min devi: 0.4295
find_ncs_matrix returns (LSQ)
| -0.4445, -0.8903, -0.09887|
| -0.893, 0.4317, 0.1271|
| -0.07049, 0.1448, -0.9869|
( -8.624, 7.402, -127.7)
INFO:: NCS chain comparison 61/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had:
mean devi: 3.7042
rms devi: 4.0859
max devi: 9.4383
min devi: 0.2858
find_ncs_matrix returns (LSQ)
| -0.7198, -0.6079, 0.3353|
| -0.5986, 0.2989, -0.7432|
| 0.3516, -0.7356, -0.579|
( 36.14, -61.4, -149.3)
INFO:: NCS chain comparison 0/67
INFO:: fill_ghost_info Constructed 3 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Ghost 2 name: "NCS found from matching Chain D onto Chain A"
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain D onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
| 0.7026, 0.6024, -0.3788|
| 0.1278, 0.4169, 0.8999|
| 0.7, -0.6807, 0.2159|
( 5.528, 36.75, -101.2)
inverse of reference matcher transformation:
| 0.7026, 0.1278, 0.7|
| 0.6024, 0.4169, -0.6807|
| -0.3788, 0.8999, 0.2159|
( 62.25, -87.53, -9.128)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
Reference matcher: 0 and 1
| -0.4445, -0.8903, -0.09887|
| -0.893, 0.4317, 0.1271|
| -0.07049, 0.1448, -0.9869|
( -8.624, 7.402, -127.7)
inverse of reference matcher transformation:
| -0.4445, -0.893, -0.07049|
| -0.8903, 0.4317, 0.1448|
| -0.09887, 0.1271, -0.9869|
( -6.223, 7.613, -127.8)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
Reference matcher: 0 and 2
| -0.7198, -0.6079, 0.3353|
| -0.5986, 0.2989, -0.7432|
| 0.3516, -0.7356, -0.579|
( 36.14, -61.4, -149.3)
inverse of reference matcher transformation:
| -0.7198, -0.5986, 0.3516|
| -0.6079, 0.2989, -0.7356|
| 0.3353, -0.7432, -0.579|
( 41.75, -69.53, -144.2)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
INFO:: There were 4.0000 maps contributing to the average
INFO:: rescaling by 0.2500
INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: -0.0008 st.d: 0.1767
Map statistics: min: -0.9977, max: 1.4866
-0.9667 1
-0.9046 3
-0.8424 8
-0.7803 10
-0.7182 37
-0.6561 102
-0.5940 196
-0.5319 490
-0.4698 1190
-0.4077 2390
-0.3456 4703
-0.2835 8981
-0.2214 16028
-0.1593 27796
-0.0972 44285
-0.0351 60780
0.0271 53651
0.0892 32327
0.1513 21048
0.2134 14284
0.2755 9269
0.3376 5945
0.3997 3629
0.4618 2439
0.5239 1480
0.5860 942
0.6481 569
0.7102 378
0.7723 239
0.8344 166
0.8965 112
0.9587 94
1.0208 50
1.0829 35
1.1450 21
1.2071 17
1.2692 5
1.3313 4
1.3934 5
1.4555 3
1.5176 0
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain D onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
| 0.7026, 0.6024, -0.3788|
| 0.1278, 0.4169, 0.8999|
| 0.7, -0.6807, 0.2159|
( 5.528, 36.75, -101.2)
inverse of reference matcher transformation:
| 0.7026, 0.1278, 0.7|
| 0.6024, 0.4169, -0.6807|
| -0.3788, 0.8999, 0.2159|
( 62.25, -87.53, -9.128)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
Reference matcher: 0 and 1
| -0.4445, -0.8903, -0.09887|
| -0.893, 0.4317, 0.1271|
| -0.07049, 0.1448, -0.9869|
( -8.624, 7.402, -127.7)
inverse of reference matcher transformation:
| -0.4445, -0.893, -0.07049|
| -0.8903, 0.4317, 0.1448|
| -0.09887, 0.1271, -0.9869|
( -6.223, 7.613, -127.8)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
Reference matcher: 0 and 2
| -0.7198, -0.6079, 0.3353|
| -0.5986, 0.2989, -0.7432|
| 0.3516, -0.7356, -0.579|
( 36.14, -61.4, -149.3)
inverse of reference matcher transformation:
| -0.7198, -0.5986, 0.3516|
| -0.6079, 0.2989, -0.7356|
| 0.3353, -0.7432, -0.579|
( 41.75, -69.53, -144.2)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
INFO:: There were 4.0000 maps contributing to the average
INFO:: rescaling by 0.2500
INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: -0.0008 st.d: 0.1767
Map statistics: min: -0.9977, max: 1.4866
-0.9667 1
-0.9046 3
-0.8424 8
-0.7803 10
-0.7182 37
-0.6561 102
-0.5940 196
-0.5319 490
-0.4698 1190
-0.4077 2390
-0.3456 4703
-0.2835 8981
-0.2214 16028
-0.1593 27796
-0.0972 44285
-0.0351 60780
0.0271 53651
0.0892 32327
0.1513 21048
0.2134 14284
0.2755 9269
0.3376 5945
0.3997 3629
0.4618 2439
0.5239 1480
0.5860 942
0.6481 569
0.7102 378
0.7723 239
0.8344 166
0.8965 112
0.9587 94
1.0208 50
1.0829 35
1.1450 21
1.2071 17
1.2692 5
1.3313 4
1.3934 5
1.4555 3
1.5176 0
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 162 NCS found from matching Chain D onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
| 0.7026, 0.6024, -0.3788|
| 0.1278, 0.4169, 0.8999|
| 0.7, -0.6807, 0.2159|
( 5.528, 36.75, -101.2)
inverse of reference matcher transformation:
| 0.7026, 0.1278, 0.7|
| 0.6024, 0.4169, -0.6807|
| -0.3788, 0.8999, 0.2159|
( 62.25, -87.53, -9.128)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
Reference matcher: 0 and 1
| -0.4445, -0.8903, -0.09887|
| -0.893, 0.4317, 0.1271|
| -0.07049, 0.1448, -0.9869|
( -8.624, 7.402, -127.7)
inverse of reference matcher transformation:
| -0.4445, -0.893, -0.07049|
| -0.8903, 0.4317, 0.1448|
| -0.09887, 0.1271, -0.9869|
( -6.223, 7.613, -127.8)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
Reference matcher: 0 and 2
| -0.7198, -0.6079, 0.3353|
| -0.5986, 0.2989, -0.7432|
| 0.3516, -0.7356, -0.579|
( 36.14, -61.4, -149.3)
inverse of reference matcher transformation:
| -0.7198, -0.5986, 0.3516|
| -0.6079, 0.2989, -0.7356|
| 0.3353, -0.7432, -0.579|
( 41.75, -69.53, -144.2)
boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302)
INFO:: There were 4.0000 maps contributing to the average
INFO:: rescaling by 0.2500
INFO:: 313712 out of 313712 (100.0000%) map points were masked out of NCS average target volume, chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: -0.0008 st.d: 0.1767
Map statistics: min: -0.9977, max: 1.4866
-0.9667 1
-0.9046 3
-0.8424 8
-0.7803 10
-0.7182 37
-0.6561 102
-0.5940 196
-0.5319 490
-0.4698 1190
-0.4077 2390
-0.3456 4703
-0.2835 8981
-0.2214 16028
-0.1593 27796
-0.0972 44285
-0.0351 60780
0.0271 53651
0.0892 32327
0.1513 21048
0.2134 14284
0.2755 9269
0.3376 5945
0.3997 3629
0.4618 2439
0.5239 1480
0.5860 942
0.6481 569
0.7102 378
0.7723 239
0.8344 166
0.8965 112
0.9587 94
1.0208 50
1.0829 35
1.1450 21
1.2071 17
1.2692 5
1.3313 4
1.3934 5
1.4555 3
1.5176 0
error (syntax error)
error (syntax error)
error (not syntax error)
Traceback (most recent call last):
File "<string>", line 1, in <module>
NameError: name 'rr_not_found_thing' is not defined
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
Symmetry available for this molecule
Molecule 171 read successfully
DEBUG:: there were 0 types with no dictionary
Entering test: OXT in restraints?
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/
There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/AR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CD.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GD.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif
There are 2 data in /lmb/home/pemsley/data/greg-data/libcheck_BCS.cif
PASS: OXT in restraints?
Entering test: Relative file name
PASS: Relative file name
Entering test: geometry distortion comparision
Good gdi < exception thrown
Good gdi > exception thrown
PASS: geometry distortion comparision
Entering test: test symm trans to origin
Got length 0.1414
PASS: test symm trans to origin
Entering test: test lsq plane
LSQ deviations: 0.0000 0.0000
PASS: test lsq plane
Entering test: test COO modification
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/
There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/AR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CD.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GD.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/hideous-OXT.pdb
PDB file /lmb/home/pemsley/data/greg-data/hideous-OXT.pdb has been read.
Spacegroup: P 21 21 21
read 9 atom
created 7 bond restraints
created 8 angle restraints
created 1 plane restraints
created 1 chiral vol restraints
created 2 torsion restraints
created 23 restraints
INFO:: make_restraints(): made 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 0.0260 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: /lmb/home/pemsley/data/greg-data/frag-2wot.pdb
PDB file /lmb/home/pemsley/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
bad residues for phi,psi calculation
bad residues for phi,psi calculation
PASS: Residues for phi,psi are close enough to be considered linked
0.0 0.0071 0.353 2.884 0.961 0.029
: 28 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.880 0.960 0.029
: 29 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.877 0.959 0.029
: 30 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.873 0.958 0.029
: 31 0.0 0.0 0.0 0. 0.0 0.0071 0.353 2.870 0.957 0.029
: 32 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.867 0.956 0.029
: 33 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.864 0.955 0.029
: 34 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.861 0.954 0.029
: 35 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.858 0.953 0.029
: 36 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.855 0.952 0.028
: 37 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.852 0.951 0.028
: 38 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.849 0.950 0.028
: 39 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.846 0.949 0.028
: 40 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.844 0.948 0.028
: 41 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.842 0.947 0.028
: 42 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.841 0.947 0.028
: 43 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.839 0.946 0.028
: 44 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.837 0.946 0.028
: 45 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.835 0.945 0.028
: 46 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.833 0.944 0.028
: 47 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.831 0.944 0.028
: 48 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.829 0.943 0.028
: 49 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.828 0.943 0.028
: 50 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.826 0.942 0.028
: 51 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.824 0.941 0.028
: 52 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.822 0.941 0.027
: 53 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.820 0.940 0.027
: 54 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.818 0.939 0.027
: 55 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.817 0.939 0.027
: 56 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.815 0.938 0.027
: 57 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.813 0.938 0.027
: 58 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.812 0.937 0.027
: 59 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.810 0.937 0.027
: 60 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.808 0.936 0.027
: 61 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.807 0.936 0.027
: 62 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.805 0.935 0.027
: 63 0.0 0.0 0.0 0. 0.0 0.0070 0.352 2.804 0.935 0.027
: 64 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.802 0.934 0.027
: 65 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.801 0.934 0.027
: 66 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.799 0.933 0.027
: 67 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.798 0.933 0.027
: 68 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.796 0.932 0.027
: 69 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.795 0.932 0.027
: 70 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.794 0.931 0.027
: 71 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.792 0.931 0.026
: 72 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.791 0.930 0.026
: 73 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.790 0.930 0.026
: 74 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.789 0.930 0.026
: 75 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.787 0.929 0.026
: 76 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.786 0.929 0.026
: 77 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.785 0.928 0.026
: 78 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.784 0.928 0.026
: 79 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.783 0.928 0.026
: 80 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.781 0.927 0.026
: 81 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.780 0.927 0.026
: 82 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.779 0.926 0.026
: 83 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.779 0.926 0.026
: 84 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.778 0.926 0.026
: 85 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.777 0.926 0.026
: 86 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.776 0.925 0.026
: 87 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.775 0.925 0.026
: 88 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.775 0.925 0.026
: 89 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.774 0.925 0.026
: 90 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.773 0.924 0.026
: 91 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.772 0.924 0.026
: 92 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.772 0.924 0.026
: 93 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.771 0.924 0.026
: 94 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.770 0.923 0.026
: 95 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.769 0.923 0.026
: 96 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.769 0.923 0.026
: 97 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.768 0.923 0.026
: 98 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.767 0.922 0.026
: 99 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.766 0.922 0.026
: 100 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.765 0.922 0.026
: 101 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.765 0.922 0.026
: 102 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.764 0.921 0.025
: 103 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.763 0.921 0.025
: 104 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.763 0.921 0.025
: 105 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.762 0.921 0.025
: 106 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.761 0.920 0.025
: 107 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.761 0.920 0.025
: 108 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.760 0.920 0.025
: 109 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.759 0.920 0.025
: 110 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.759 0.920 0.025
: 111 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.758 0.919 0.025
: 112 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.757 0.919 0.025
: 113 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.757 0.919 0.025
: 114 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.756 0.919 0.025
: 115 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.756 0.919 0.025
: 116 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.755 0.918 0.025
: 117 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.755 0.918 0.025
: 118 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.754 0.918 0.025
: 119 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.754 0.918 0.025
: 120 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.753 0.918 0.025
: 121 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.753 0.918 0.025
: 122 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.752 0.917 0.025
: 123 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.752 0.917 0.025
: 124 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.751 0.917 0.025
: 125 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.751 0.917 0.025
: 126 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.751 0.917 0.025
: 127 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.750 0.917 0.025
: 128 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.750 0.917 0.025
: 129 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.750 0.917 0.025
: 130 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.749 0.916 0.025
: 131 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.749 0.916 0.025
: 132 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.748 0.916 0.025
: 133 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.748 0.916 0.025
: 134 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.748 0.916 0.025
: 135 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.747 0.916 0.025
: 136 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.747 0.916 0.025
: 137 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.747 0.916 0.025
: 138 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.746 0.915 0.025
: 139 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.746 0.915 0.025
: 140 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.746 0.915 0.025
: 141 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.745 0.915 0.025
: 142 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.745 0.915 0.025
: 143 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.744 0.915 0.025
: 144 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.744 0.915 0.025
: 145 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.744 0.915 0.025
: 146 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.744 0.915 0.025
: 147 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.743 0.914 0.025
: 148 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.743 0.914 0.025
: 149 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.743 0.914 0.024
: 150 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.742 0.914 0.024
: 151 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.742 0.914 0.024
: 152 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.742 0.914 0.024
: 153 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.741 0.914 0.024
: 154 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.741 0.914 0.024
: 155 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.741 0.914 0.024
: 156 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.741 0.914 0.024
: 157 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.740 0.913 0.024
: 158 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.740 0.913 0.024
: 159 0.0 0.0 0.0 0. 0.0 0.0070 0.351 2.740 0.913 0.024
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
: Refmac_5.8.0131: End of Refmac_5.8.0131
:Times: User: 4.2s System: 0.1s Elapsed: 0:04
:</pre>
:</html>
:<!--SUMMARY_END--></FONT></B>
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: #<unspecified>
PASS: Many Molecules - Ligand Fitting
Entered testcase - flip residue (around eigen vectors)
distance: 4.05825923997285
distance d2: 4.95113364632015e-7
PASS: flip residue (around eigen vectors)
Entered testcase - Test dipole
info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0)
PASS: Test dipole
Entered testcase - Reading new dictionary restraints replaces
PASS: Reading new dictionary restraints replaces
Ended 03-ligand.scm
Running 04-cootaneer.scm ...
Entered testcase - Assignment of new PIR sequence overwrites old assignment
debug seq: ("A" . "ACDEFGHIKLMNPQ")
PASS: Assignment of new PIR sequence overwrites old assignment
Entered testcase - Cootaneer Beta Strand
Cootaneering: imol 140 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf ""
PASS: Cootaneer Beta Strand
Ended 04-cootaneer.scm
Running 05-rna-ghosts.scm ...
Entered testcase - RNA NCS Ghosts
There are 8 residues in chain "A"
There are 8 residues in chain "B"
PASS: RNA NCS Ghosts
Ended 05-rna-ghosts.scm
Running 06-ssm.scm ...
Entered testcase - SSM - Frank von Delft's Example
PASS: SSM - Frank von Delft's Example
Entered testcase - SSM - Alice Dawson's Example
0 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
2 "/lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb"
3 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
4 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
5 "/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
6 "test-3hfl.map"
7 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
8 "mainchain"
9 "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb"
10 "atom selection from tutorial-add-terminal-1-test.pdb"
11 "/lmb/home/pemsley/data/greg-data/frag-2wot.pdb"
12 "sphere selection from tutorial-modern.pdb"
14 "/lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb"
15 "/lmb/home/pemsley/data/greg-data/res098.pdb"
16 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
17 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
18 "/lmb/home/pemsley/data/greg-data/pdb3knw.ent"
19 "/lmb/home/pemsley/data/greg-data/pdb1py3.ent"
22 "/lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb"
23 "/lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb"
24 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
25 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
26 "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb"
27 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
28 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
29 "/lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb"
30 "/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb"
31 "Copy_of_/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb"
32 "/lmb/home/pemsley/data/greg-data/coords-B3A.pdb"
33 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT"
34 "/lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb"
35 "/lmb/home/pemsley/data/greg-data/val.pdb"
36 "/lmb/home/pemsley/data/greg-data/2yie-frag.pdb"
37 "/lmb/home/pemsley/data/greg-data/4f8g.pdb"
38 "/lmb/home/pemsley/data/greg-data/4f8g.pdb"
39 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
40 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
41 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
42 "Generic Masked Map"
43 "difference-map"
44 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
45 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
46 "averaged-map"
47 "difference-map"
48 "/lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb"
49 "/lmb/home/pemsley/data/greg-data/monomer-VAL.pdb"
50 "/lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb"
51 "atom selection from tutorial-modern.pdb"
52 "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb"
53 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
54 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
55 "atom selection from tutorial-modern.pdb"
56 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
57 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
58 "/lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb"
59 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
60 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
61 "/lmb/home/pemsley/data/greg-data/pdb3hfl.ent"
62 "/lmb/home/pemsley/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_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
68 "/lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb"
69 "/lmb/home/pemsley/data/greg-data/tm+some-waters.pdb"
70 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
71 "/lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb"
72 "/lmb/home/pemsley/data/greg-data/pathological-water-test.pdb"
73 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
74 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
75 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
76 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
77 "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent"
78 "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb"
79 "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb"
80 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_77"
81 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
82 "Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
83 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
84 "/lmb/home/pemsley/data/greg-data/pdb1py3.ent"
85 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
86 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
87 "/lmb/home/pemsley/data/greg-data/2goz-manip.pdb"
88 "/lmb/home/pemsley/data/greg-data/HOF.RES"
89 "/lmb/home/pemsley/data/greg-data/hollander.ins"
92 "/lmb/home/pemsley/data/greg-data/insulin.fcf"
93 "atom selection from insulin.res"
94 "atom selection from insulin.res"
96 "/lmb/home/pemsley/data/greg-data/horma-p21.res"
97 "new-horma.ins"
98 "/lmb/home/pemsley/data/greg-data/crash.hat"
99 "coot-ccp4/monomer-3GP.pdb"
100 "/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb"
101 "/lmb/home/pemsley/data/greg-data/test-LIG.pdb"
102 "/lmb/home/pemsley/data/greg-data/test-LIG.pdb"
103 "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb"
104 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb"
105 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb"
106 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb"
107 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb"
108 "Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb"
109 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb"
110 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT"
111 "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT"
112 "Masked (by protein)"
113 "Fitted ligand #0-0"
114 "Fitted ligand #0-1"
115 "Fitted ligand #0-2"
116 "Fitted ligand #1-0"
117 "Fitted ligand #1-1"
118 "Fitted ligand #2-0"
119 "Fitted ligand #2-1"
120 "Fitted ligand #2-2"
121 "Fitted ligand #2-3"
122 "Fitted ligand #3-0"
123 "Fitted ligand #3-1"
124 "Fitted ligand #3-2"
125 "Fitted ligand #4-0"
126 "Fitted ligand #5-0"
127 "Fitted ligand #5-1"
128 "Fitted ligand #6-0"
129 "Fitted ligand #6-1"
130 "Fitted ligand #7-0"
131 "Fitted ligand #8-0"
132 "Fitted ligand #8-1"
133 "Fitted ligand #9-0"
134 "Fitted ligand #9-1"
135 "Fitted ligand #9-2"
136 "coot-ccp4/monomer-3GP.pdb"
137 "Copy_of_coot-ccp4/monomer-3GP.pdb"
138 "/lmb/home/pemsley/data/greg-data/dipole-residues.pdb"
139 "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb"
140 "/lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb"
141 "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
142 "Ideal-A-form-RNA"
145 "/lmb/home/pemsley/data/greg-data/1wly.pdb"
146 "/lmb/home/pemsley/data/greg-data/1yb5.pdb"
PASS: SSM - Alice Dawson's Example
Entered testcase - SSM by atom selection [JED Example]
PASS: SSM by atom selection [JED Example]
Ended 06-ssm.scm
Running 07-ncs.scm ...
Entered testcase - NCS maps test
PASS: NCS maps test
Entered testcase - NCS chains info
NCS info: (("A" "B"))
PASS: NCS chains info
Entered testcase - NCS deviation info
PASS: NCS deviation info
Entered testcase - NCS Residue Range copy
PASS: NCS Residue Range copy
Entered testcase - NCS Residue Range edit to all chains
result: (#t #t)
PASS: NCS Residue Range edit to all chains
Entered testcase - Manual NCS ghosts generates correct NCS chain ids
NCS ghost chain IDs pre: (("B" "A" "C" "D"))
NCS ghost chain IDs post: (("B" "A" "C" "D"))
PASS: Manual NCS ghosts generates correct NCS chain ids
Entered testcase - NCS maps overwrite existing maps
==== test-name: "Map 162 NCS found from matching Chain B onto Chain A" n-matchers: 2
==== test-name: "Map 162 NCS found from matching Chain C onto Chain A" n-matchers: 2
==== test-name: "Map 162 NCS found from matching Chain D onto Chain A" n-matchers: 2
PASS: NCS maps overwrite existing maps
Ended 07-ncs.scm
Running 08-utils.scm ...
Entered testcase - Test key symbols
WARNING:: could not find key-sym-code for "missing key"
PASS: Test key symbols
Entered testcase - Test running a Python function
test_val_2 passed
test_val_3 passed
PASS: Test running a Python function
Entered testcase - Internal/External Molecule Numbers match
PASS: Internal/External Molecule Numbers match
Entered testcase - spacegroup operators to space group conversion
PASS: spacegroup operators to space group conversion
Ended 08-utils.scm
Running 09-internal.scm ...
Entered testcase - Test internal functions
PASS: Test internal functions
Ended 09-internal.scm
=== greg-tests Summary ===
# of testcases attempted 117
# of expected passes 117
# of expected failures 0
# of unexpected passes 0
# of unexpected failures 0
# of unresolved testcases 0
# of unsupported testcases 0
# of untested testcases 0
Loading greg-tests/end.grg ...
Loaded greg-tests/end.grg
=== Summary of all tests ===
# of tools 1
# of testcases attempted 117
# of expected passes 117
# of expected failures 0
# of unexpected passes 0
# of unexpected failures 0
# of unresolved testcases 0
# of unsupported testcases 0
# of untested testcases 0
# of files abandoned 0
test_coot: coot test passed