testing with greg
testing with greg
currently we are here:
/home/paule/autobuild/building/emsley-vm-debian-7-7_2018-05-14__T10_36_02/test-tar/coot-Linux-x86_64-debian-gnu-linux-8-pre-release-gtk2-python
Mon 14 May 11:46:22 BST 2018
WARNING:: ccp4 setup file setup-ccp4 does not exist.
/home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/
INFO:: Reading coordinate file: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/standard-residues.pdb
PDB file /home/paule/autobuild/Linux-emsley-vm-debian-7-7-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
INFO:: coot.py imported
Running python script /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Paul, Welcome to Coot version 0.8.9.2-pre
[1m(set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.8.9.2-pre")[0m
BL WARNING:: CCP4_BIN not defined!
BL INFO:: we don't search the whole disk for probe
BL WARNING:: We cannot find probe anywhere! Program probe won't run!
BL WARNING:: CCP4_BIN not defined!
BL INFO:: we don't search the whole disk for reduce
BL WARNING:: We cannot find reduce anywhere! Program reduce won't run!
[1m(use-graphics-interface-state)[0m
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
[1m(use-graphics-interface-state)[0m
[1m(set-display-intro-string "Good morning root. Welcome to Coot 0.8.9.2-pre")[0m
[1m(set-display-lists-for-maps 0)[0m
load /home/paule/.coot-preferences/coot-preferences.scm
[1m(set-filter-fileselection-filenames 0)[0m
[1m(unset-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 1.00)[0m
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
INFO:: There are 1 command line scripts to run
command-line-greg.scm
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 0 read successfully
DEBUG:: there were 0 types with no dictionary
Molecule number -5 is not a valid model molecule
INFO:: Reading coordinate file: /home/paule/data/greg-data/2WF6.cif
mmCIF file /home/paule/data/greg-data/2WF6.cif has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 1 read successfully
DEBUG:: there were 3 types with no dictionary
in new_molecule_by_atom_selection Something bad happened - No atoms selected
INFO:: Reading coordinate file: /home/paule/data/greg-data/ins-code-fragment-pre.pdb
PDB file /home/paule/data/greg-data/ins-code-fragment-pre.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 2 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Creating directory coot-backup
INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_May_14_11:46:25_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_May_14_11:46:25_2018_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_May_14_11:46:25_2018_modification_2.pdb.gz
WARNING:: Error reading bogus.map
Read map bogus.map failed
WARNING:: Can't find file bogus.mtz
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.034 seconds to read MTZ file
INFO:: 0.011 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.04051e-09
Map sigma: ....... 0.311501
Map maximum: ..... 2.97757
Map minimum: ..... -0.875045
INFO:: 0.014 seconds for contour map
INFO:: 0.081 seconds in total
WARNING:: file xx-missing.mtz does not exist
>>>>>> CCP4 library signal library_file:End of File (Error)
raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 0:Success (Error)
raised in ccp4_file_rarch <<<<<<
>>>>>> CCP4 library signal library_file:End of File (Error)
raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 0:Success (Error)
raised in ccp4_file_readint <<<<<<
>>>>>> System signal 0:Success (Error)
raised in ccp4_file_read <<<<<<
>>>>>> CCP4 library signal library_file:End of File (Error)
raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 0:Success (Error)
raised in ccp4_file_readchar <<<<<<
>>>>>> CCP4 library signal mtz:Read failed (Error)
raised in MtzGet <<<<<<
CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz
INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz
INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.03 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.04051e-09
Map sigma: ....... 0.311501
Map maximum: ..... 2.97757
Map minimum: ..... -0.875045
INFO:: 0.013 seconds for contour map
INFO:: 0.065 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz
Number of OBSERVED reflections: 17920
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 64, 96, 90)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0.006 seconds to initialize map
INFO:: 0.013 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 7.46232e-11
Map sigma: ....... 0.260405
Map maximum: ..... 1.71787
Map minimum: ..... -1.03389
INFO:: 0.003 seconds for contour map
INFO:: 0.051 seconds in total
INFO:: map file type was determined to be CCP4 type
INFO:: attempting to read CCP4 map: test-3hfl.map
Map statistics: mean: 7.46232e-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 1
1.75226 0
INFO:: n grid points: 276480
INFO:: mean before filtering: 7.46232e-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: ........ 4.053e-06
Map rmsd: ........ 0.2605
Map maximum: ..... 1.718
Map minimum: ..... -1.034
WARNING:: Error reading .
. is a directory.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 7 read successfully
DEBUG:: there were 0 types with no dictionary
/home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures successfully opened
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
4 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
14 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
29 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
218 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
24 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
137 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
35 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
543 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
228 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb
There was an error reading /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb.
ERROR 42 READ: Duplicate sequence number and insertion code.
LINE #868
ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 C
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
45 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
54 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
174 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
75 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
318 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
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142 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
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326 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
72 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
13 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
294 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
23 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
520 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
127 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
136 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
51 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
108 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
119 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
131 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
64 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
149 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
56 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
226 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
155 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
143 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
364 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
247 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
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52 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
145 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
106 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
494 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
68 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
33 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
140 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
172 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
20 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
208 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
171 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
123 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
411 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
205 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
349 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
9 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
0 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
129 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
INFO:: 8375 fragments found in total of which 0 were 5 peptides
target fragment start res: 10 had 29 db fragment hits, ilength=6
target fragment start res: 13 had 1772 db fragment hits, ilength=6
breaking out of match_target_fragment 6 with iresno= 16
merge fragments 10 to 20 with 2 fit sets to merge
The merging is complete
mainchain_fragment from 10 to 20
done mainchain_fragment
successfully set cell and symmetry
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb
PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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
fitting terminal residue with 1000 random trials
called fit_terminal_residue_generic() residue-seqnum: 1 offset: -1
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_May_14_11:46:27_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Mon_May_14_11:46:27_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb
PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:27_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:27_2018_modification_1.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:27_2018_modification_2.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/rotamer-test-fragment.pdb
PDB file /home/paule/data/greg-data/rotamer-test-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 14 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading rotamer probability tables...
primitive chis: Failure to find correct atom quads in residue atoms
quad needed: : N : : CA : : CB : : OG1:
INFO:: un altconfed rotamer with no chis [spec: 1 "A" 16 ""]
INFO:: Reading coordinate file: /home/paule/data/greg-data/res098.pdb
PDB file /home/paule/data/greg-data/res098.pdb has been read.
Spacegroup: P 41 21 2
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 15 read successfully
DEBUG:: there were 0 types with no dictionary
created 6 bond restraints
created 6 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 13 restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints:
2 bond links
7 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 9 non-bonded restraints
initial distortion_score: 26.65
Initial RMS Z values
bonds: 0.2292
angles: 0.4339
torsions: N/A
planes: 0.3222
non-bonded: 0
chiral vol: 0.1627
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 149) at 9.945
Final Estimated RMS Z Scores:
bonds: 0.09591
angles: 0.6652
torsions: N/A
planes: 0.6486
non-bonded: 0
chiral vol: 0.5914
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 2.432
Removing idle function -1
debug:: restraints results 1 5
INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Mon_May_14_11:46:28_2018_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 16 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.019 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.015 seconds for contour map
INFO:: 0.065 seconds in total
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:28_2018_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0
debug:: split_residue() returned 0 ""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:28_2018_modification_1.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 11.75
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3knw.ent
PDB file /home/paule/data/greg-data/pdb3knw.ent has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 30 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
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 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3knw.ent_Mon_May_14_11:46:28_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent
PDB file /home/paule/data/greg-data/pdb1py3.ent has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
INFO:: NCS chain comparison 91/204
INFO:: NCS chain comparison 90/204
INFO:: NCS chain comparison 175/179
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain C onto Chain B"
Molecule 19 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1py3.ent_Mon_May_14_11:46:28_2018_modification_0.pdb.gz
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE
INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP
Good morning root. Welcome to Coot 0.8.9.2-pre.
=== greg-tests tests ===
Loading greg-tests/begin.grg ...
===============================================================
==================== Testing ==================================
===============================================================
Loaded greg-tests/begin.grg
Running 01-pdb+mtz.scm ...
Entered testcase - Post Go To Atom no molecules
PASS: Post Go To Atom no molecules
Entered testcase - Close bad molecule
PASS: Close bad molecule
Entered testcase - Read coordinates test
PASS: Read coordinates test
Entered testcase - New molecule from bogus molecule
PASS: New molecule from bogus molecule
Entered testcase - Don't crash on empty NCS from mmCIF file
closing molecule number 1
PASS: Don't crash on empty NCS from mmCIF file
Entered testcase - New molecule from bogus atom selection
INFO:: pre-n-molecules 2 post-n-molecules 2
PASS: New molecule from bogus atom selection
Entered testcase - ins code change and Goto atom over an ins code break
pre and post ins codes: "" "A"
pass: ("A" 68 "" " CA ")
pass: ("A" 68 "B" " CA ")
pass: ("A" 68 "B" " CA ")
pass: ("A" 68 "B" " CA ")
pass: ("A" 68 "A" " CA ")
pass: ("A" 68 "" " CA ")
pass: ("A" 66 "" " CA ")
PASS: ins code change and Goto atom over an ins code break
Entered testcase - Read a bogus map
PASS: Read a bogus map
Entered testcase - Read MTZ test
PASS: Read MTZ test
Entered testcase - Auto-read bad MTZ test
got status: #()
got status: #()
PASS: Auto-read bad MTZ test
Entered testcase - Map Sigma
INFO:: map sigmas 0.311501026153564 #f
PASS: Map Sigma
Entered testcase - Another Level Test
PASS: Another Level Test
Entered testcase - Sharpen map from map
PASS: Sharpen map from map
Entered testcase - db-main makes mainchain
PASS: db-main makes mainchain
Entered testcase - Set Atom Attribute Test
PASS: Set Atom Attribute Test
Entered testcase - Add Terminal Residue Test
PASS: Add Terminal Residue Test
Entered testcase - Adding residue by phi psi, no crash
PASS: Adding residue by phi psi, no crash
Entered testcase - Select by Sphere
Sphere mol: there are 4 residues in chain "B"
Found 20 sphere atoms
PASS: Select by Sphere
Entered testcase - Test Views
PASS: Test Views
Entered testcase - Label Atoms and Delete
PASS: Label Atoms and Delete
Entered testcase - Rotamer outliers
PASS: Rotamer outliers
Entered testcase - Alt Conf Occ Sum Reset
For atom " CE " "A" returning occ 0.699999988079071
For atom " CE " "B" returning occ 0.200000002980232
For atom " NZ " "A" returning occ 0.699999988079071
For atom " NZ " "B" returning occ 0.200000002980232
For atom " CE " "A" returning occ 0.699999988079071
For atom " CE " "B" returning occ 0.200000002980232
For atom " NZ " "A" returning occ 0.699999988079071
For atom " NZ " "B" returning occ 0.200000002980232
test for closeness: 1.79999998211861 1.79999998211861
PASS: Alt Conf Occ Sum Reset
Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue
PASS: Correct occupancies after auto-fit rotamer on alt-confed residue
Entered testcase - Rotamers work on MSE
se-1: (("SE " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746))
se-2: (("SE " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616))
PASS: Rotamers work on MSE
Entered testcase - Hs are correctly swapped on a TYR
bond-length-within-tolerance? bond-length 0.93069991132425 with target 0.93 and tolerance 0.02 for atom ((" CD1" "") (1.0 (22.3700008392334 0.288300007581711 0.351099997758865 0.210400000214577 0.0551000013947487 0.0124000003561378 0.00350000010803342) " C" "") (61.2610015869141 -13.2200002670288 1.25)) is ((" HD1" "") (1.0 22.7800006866455 " H" "") (61.4099998474121 -12.8690004348755 2.09899997711182))
bond-length-within-tolerance? bond-length 0.930136198469449 with target 0.93 and tolerance 0.02 for atom ((" CD2" "") (1.0 (24.4099998474121 0.258899986743927 0.405699998140335 0.262800008058548 0.0627999976277351 -0.0269000008702278 -0.00970000028610229) " C" "") (59.9500007629395 -13.3459997177124 -0.740000009536743)) is ((" HD2" "") (1.0 24.3099994659424 " H" "") (59.2050018310547 -13.0869998931885 -1.23300004005432))
bond-length-within-tolerance? bond-length 0.930888837109095 with target 0.93 and tolerance 0.02 for atom ((" CE1" "") (1.0 (22.1599998474121 0.280600011348724 0.314999997615814 0.246199995279312 0.0603000000119209 -0.0186000000685453 -0.0172000005841255) " C" "") (62.1650009155273 -14.1079998016357 0.726000010967255)) is ((" HE1" "") (1.0 22.1200008392334 " H" "") (62.9140014648438 -14.3520002365112 1.22200000286102))
bond-length-within-tolerance? bond-length 0.929591631283786 with target 0.93 and tolerance 0.02 for atom ((" CE2" "") (1.0 (23.9099998474121 0.281399995088577 0.359200000762939 0.267500013113022 0.0529999993741512 -0.0285000000149012 -0.0131999999284744) " C" "") (60.8559989929199 -14.2670001983643 -1.29900002479553)) is ((" HE2" "") (1.0 23.5400009155273 " H" "") (60.7249984741211 -14.6049995422363 -2.15499997138977))
INFO:: 25 residues had their atoms swapped
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 20 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.019 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.014 seconds for contour map
INFO:: 0.065 seconds in total
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:28_2018_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0
debug:: split_residue() returned 0 ""
INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-pepflip-test.pdb
PDB file /home/paule/data/greg-data/alt-conf-pepflip-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 22 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-pepflip-test.pdb_Mon_May_14_11:46:29_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb
PDB file /home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 0x7b7eab0
omega: 1 12.77 degrees
INFO This is a CIS peptide - making it TRANS
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_May_14_11:46:29_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_May_14_11:46:29_2018_modification_1.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 11 A 12
INFO:: mutate 11 A to a GLY
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_May_14_11:46:29_2018_modification_2.pdb.gz
created 10 bond restraints
created 10 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 21 restraints
INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A
Link restraints:
1 bond links
4 angle links
2 plane links
1 trans-peptide links
0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints:
2 bond links
7 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 27 non-bonded restraints
initial distortion_score: 4186
Initial RMS Z values
bonds: 15.46
angles: 7.124
torsions: N/A
planes: 2.181
non-bonded: 126.2
chiral vol: 3.045
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 52) at -4777
Final Estimated RMS Z Scores:
bonds: 0.9811
angles: 0.7821
torsions: N/A
planes: 2.655
non-bonded: 0.1506
chiral vol: 0.1462
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 3.364
Removing idle function -1
Refinement elapsed time: 0.011
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_May_14_11:46:29_2018_modification_3.pdb.gz
INFO:: replace_coords: 11 atoms updated.
INFO:: mutate 11 A to a LEU
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_May_14_11:46:29_2018_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_May_14_11:46:29_2018_modification_5.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 8.45
created 14 bond restraints
created 16 angle restraints
created 0 plane restraints
created 2 chiral vol restraints
created 32 restraints
INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A
Link restraints:
1 bond links
4 angle links
2 plane links
1 trans-peptide links
0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints:
2 bond links
7 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 63 non-bonded restraints
initial distortion_score: -5905
Initial RMS Z values
bonds: 0.9632
angles: 1.612
torsions: N/A
planes: 3.298
non-bonded: 0.4905
chiral vol: 0.4295
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 75) at -6029
Final Estimated RMS Z Scores:
bonds: 0.9458
angles: 0.7027
torsions: N/A
planes: 2.721
non-bonded: 0.06956
chiral vol: 0.1094
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 3.45
Removing idle function -1
Refinement elapsed time: 0.009
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_May_14_11:46:29_2018_modification_6.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 24 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.014 seconds for contour map
INFO:: 0.065 seconds in total
created 5 bond restraints
created 4 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 10 restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 6 non-bonded restraints
initial distortion_score: -2329
Initial RMS Z values
bonds: 1.674
angles: 1.07
torsions: N/A
planes: 0.6113
non-bonded: 9.246
chiral vol: 1.462
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 1) at -2443
Final Estimated RMS Z Scores:
bonds: 0.9903
angles: 1.019
torsions: N/A
planes: 0.4702
non-bonded: 1.066
chiral vol: 0.892
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 3.663
Removing idle function -1
Refinement elapsed time: 0.006
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:29_2018_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb
PDB file /home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_May_14_11:46:29_2018_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0
debug:: split_residue() returned 0 ""
INFO:: created 81 restraints
created 34 bond restraints
created 39 angle restraints
created 2 plane restraints
created 6 chiral vol restraints
Link restraints:
2 bond links
6 angle links
0 plane links
4 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
5 bond links
15 angle links
10 plane links
5 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 1543 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -1.565e+04
Initial RMS Z values
bonds: 1.743
angles: 1.268
torsions: N/A
planes: 0.8383
non-bonded: 0.0006843
chiral vol: 0.8944
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 33) at -1.604e+04
Final Estimated RMS Z Scores:
bonds: 1.009
angles: 0.6514
torsions: N/A
planes: 0.5838
non-bonded: 2.094e-05
chiral vol: 0.2395
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 3.901
Removing idle function -1
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_May_14_11:46:29_2018_modification_1.pdb.gz
INFO:: replace_coords: 39 atoms updated.
INFO:: created 84 restraints
created 36 bond restraints
created 40 angle restraints
created 3 plane restraints
created 5 chiral vol restraints
Link restraints:
4 bond links
12 angle links
8 plane links
3 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 1247 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -7144
Initial RMS Z values
bonds: 0.9807
angles: 1.018
torsions: N/A
planes: 1.787
non-bonded: 5.295
chiral vol: 10.28
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 58) at -1.565e+04
Final Estimated RMS Z Scores:
bonds: 1.947
angles: 1.786
torsions: N/A
planes: 1.613
non-bonded: 0.05005
chiral vol: 1.769
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 4.061
Removing idle function -1
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_May_14_11:46:29_2018_modification_2.pdb.gz
INFO:: replace_coords: 41 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 27 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.014 seconds for contour map
INFO:: 0.065 seconds in total
created 29 bond restraints
created 32 angle restraints
created 2 plane restraints
created 4 chiral vol restraints
created 67 restraints
INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A
Link restraints:
3 bond links
9 angle links
6 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 315 non-bonded restraints
initial distortion_score: -5944
Initial RMS Z values
bonds: 0.9358
angles: 1.058
torsions: N/A
planes: 1.985
non-bonded: 11.39
chiral vol: 11.48
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 1) at -1.155e+04
Final Estimated RMS Z Scores:
bonds: 1.881
angles: 1.715
torsions: N/A
planes: 2.07
non-bonded: 0.07565
chiral vol: 1.826
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 4.321
Removing idle function -1
Refinement elapsed time: 0.049
----------------------------------------------
----------------------------------------------
ERROR:: B: last_restraints no cleared up
----------------------------------------------
----------------------------------------------
created 29 bond restraints
created 32 angle restraints
created 2 plane restraints
created 4 chiral vol restraints
created 67 restraints
INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A
Link restraints:
3 bond links
9 angle links
6 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 315 non-bonded restraints
initial distortion_score: 1736
Initial RMS Z values
bonds: 0.9358
angles: 1.058
torsions: N/A
planes: 1.985
non-bonded: 11.39
chiral vol: 11.48
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 65) at -3217
Final Estimated RMS Z Scores:
bonds: 0.7211
angles: 0.8753
torsions: N/A
planes: 1.699
non-bonded: 0.006122
chiral vol: 0.8311
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 4.412
Removing idle function -1
Refinement elapsed time: 0.09
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 29 read successfully
DEBUG:: there were 0 types with no dictionary
----------------------------------------------
----------------------------------------------
ERROR:: A: last_restraints no cleared up
----------------------------------------------
----------------------------------------------
INFO:: created 52 restraints
created 23 bond restraints
created 25 angle restraints
created 0 plane restraints
created 4 chiral vol restraints
Link restraints:
3 bond links
8 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
3 bond links
9 angle links
6 plane links
3 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 764 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -4158
Initial RMS Z values
bonds: 1.62
angles: 1.009
torsions: N/A
planes: 0.7374
non-bonded: 0.02561
chiral vol: 0.5795
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 44) at -4313
Final Estimated RMS Z Scores:
bonds: 0.3784
angles: 0.7486
torsions: N/A
planes: 0.3959
non-bonded: 0.002483
chiral vol: 0.4642
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 4.599
Removing idle function -1
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:30_2018_modification_0.pdb.gz
INFO:: replace_coords: 27 atoms updated.
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=0.3089332536598
PASS: Refine Zone with Alt conf
Entered testcase - Sphere Refine
======= got bond length 1.28254206006481
PASS: Sphere Refine
Entered testcase - Refinement gives useful results
refinement results: ("" 0 (("Bonds" "Bonds: 1.881" 1.88061583042145) ("Angles" "Angles: 1.715" 1.71482503414154) ("Planes" "Planes: 2.070" 2.06990146636963) ("Non-bonded" "Non-bonded: 0.275" 0.275054275989532) ("Chirals" "Chirals: 1.826" 1.82564008235931)))
ow factor: 1.87274560332298
INFO:: setting refinement weight to 17.1077808409876
refinement results: ("" 0 (("Bonds" "Bonds: 0.721" 0.72113424539566) ("Angles" "Angles: 0.875" 0.87533050775528) ("Planes" "Planes: 1.699" 1.69930875301361) ("Non-bonded" "Non-bonded: 0.078" 0.0782448276877403) ("Chirals" "Chirals: 0.831" 0.831129372119904)))
ow factor: 1.03172571957111
PASS: Refinement gives useful results
Entered testcase - Neighbour-Refine doesn't destroy disulfide bonds
bond-length-within-tolerance? bond-length 2.0321570623497 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6310691833496 27.4846820831299 11.247278213501)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7477836608887 27.0910205841064 9.45996189117432))
INFO:: created 52 restraints
created 23 bond restraints
created 25 angle restraints
created 0 plane restraints
created 4 chiral vol restraints
Link restraints:
3 bond links
8 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
3 bond links
9 angle links
6 plane links
3 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 763 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -4313
Initial RMS Z values
bonds: 0.3784
angles: 0.7486
torsions: N/A
planes: 0.3959
non-bonded: 0.002486
chiral vol: 0.4642
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 1) at -4313
Final Estimated RMS Z Scores:
bonds: 0.3786
angles: 0.7488
torsions: N/A
planes: 0.3952
non-bonded: 0.002518
chiral vol: 0.4657
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 4.631
Removing idle function -1
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:30_2018_modification_1.pdb.gz
INFO:: replace_coords: 27 atoms updated.
bond-length-within-tolerance? bond-length 2.03206704528906 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6309757232666 27.4847221374512 11.247200012207)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7479362487793 27.0910339355469 9.45987033843994))
INFO:: Reading coordinate file: /home/paule/data/greg-data/alt-conf-waters.pdb
PDB file /home/paule/data/greg-data/alt-conf-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 30 read successfully
DEBUG:: there were 0 types with no dictionary
masking....masking done
INFO:: backup file coot-backup/_home_paule_data_greg-data_alt-conf-waters.pdb_Mon_May_14_11:46:30_2018_modification_0.pdb.gz
INFO:: replace_coords: 1 atoms updated.
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring
INFO:: Reading coordinate file: /home/paule/data/greg-data/backrub-fragment.pdb
PDB file /home/paule/data/greg-data/backrub-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 31 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Mon_May_14_11:46:30_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Mon_May_14_11:46:30_2018_modification_1.pdb.gz
INFO:: replace_coords: 14 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/coords-B3A.pdb
PDB file /home/paule/data/greg-data/coords-B3A.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 33 read successfully
DEBUG:: there were 1 types with no dictionary
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 11 restraints
INFO:: make_restraints(): made 5 non-bonded restraints
initial distortion_score: 2.951
Initial RMS Z values
bonds: 0.6619
angles: 0.3737
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.25
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 23) at 4.802e-05
Final Estimated RMS Z Scores:
bonds: 0.001418
angles: 0.002701
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.001214
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 5.029
Removing idle function -1
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_May_14_11:46:30_2018_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/lib-B3A.cif" not found.
init_refmac_mon_lib /home/paule/data/greg-data/lib-B3A.cif had no bond restraints
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 11 restraints
INFO:: make_restraints(): made 5 non-bonded restraints
initial distortion_score: 4.802e-05
Initial RMS Z values
bonds: 0.001418
angles: 0.002701
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.001214
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 1) at 3.529e-05
Final Estimated RMS Z Scores:
bonds: 0.0003425
angles: 0.002614
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.0007295
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 5.127
Removing idle function -1
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_May_14_11:46:30_2018_modification_1.pdb.gz
INFO:: replace_coords: 6 atoms updated.
Welcome to Coot
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 11 restraints
INFO:: make_restraints(): made 5 non-bonded restraints
initial distortion_score: 3.018
Initial RMS Z values
bonds: 0.6708
angles: 0.3753
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.2536
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 16) at 1.587e-06
Final Estimated RMS Z Scores:
bonds: 0.0003952
angles: 0.0003942
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.0001708
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 5.237
Removing idle function -1
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_May_14_11:46:30_2018_modification_2.pdb.gz
INFO:: replace_coords: 6 atoms updated.
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.013 seconds for contour map
INFO:: 0.064 seconds in total
INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible.
INFO:: Reading coordinate file: /home/paule/data/greg-data/test-TER-OXT.pdb
PDB file /home/paule/data/greg-data/test-TER-OXT.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 35 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_test-TER-OXT.pdb_Mon_May_14_11:46:31_2018_modification_0.pdb.gz
Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.13,-9.09,14.92) B-factor: 45
debug:: add_OXT_to_residue() returns istat 1
WARNING:: This residue already has an OXT - aborting
debug:: add_OXT_to_residue() returns istat 0
INFO:: Reading coordinate file: /home/paule/data/greg-data/val.pdb
PDB file /home/paule/data/greg-data/val.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 36 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: mutate 3 C to a HIS
INFO:: backup file coot-backup/_home_paule_data_greg-data_val.pdb_Mon_May_14_11:46:31_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/2yie-frag.pdb
PDB file /home/paule/data/greg-data/2yie-frag.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 37 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_2yie-frag.pdb_Mon_May_14_11:46:31_2018_modification_0.pdb.gz
INFO:: 6 matched atoms had:
mean devi: 0.04043
rms devi: 0.04717
max devi: 0.08328
min devi: 0.01301
INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb
PDB file /home/paule/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 2 biomt matrices
Molecule 38 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_May_14_11:46:31_2018_modification_0.pdb.gz
INFO:: 6 matched atoms had:
mean devi: 0.04346
rms devi: 0.04779
max devi: 0.07399
min devi: 0.01477
INFO:: Reading coordinate file: /home/paule/data/greg-data/4f8g.pdb
PDB file /home/paule/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 2 biomt matrices
Molecule 39 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_May_14_11:46:31_2018_modification_0.pdb.gz
INFO:: 6 matched atoms had:
mean devi: 0.03945
rms devi: 0.04446
max devi: 0.06949
min devi: 0.01513
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.019 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.012 seconds for contour map
INFO:: 0.062 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.2
INFO grid sampling...Nuvw = ( 160, 192, 96)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0.032 seconds to initialize map
INFO:: 0.038 seconds for FFT
INFO:: 0.007 seconds for statistics
Map mean: ........ 1.185e-09
Map sigma: ....... 0.3115
Map maximum: ..... 3.052
Map minimum: ..... -0.9217
INFO:: 0.032 seconds for contour map
INFO:: 0.138 seconds in total
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 42 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: 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 0
3.026 1
PASS: Neighbour-Refine doesn't destroy disulfide bonds
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 0.928160607814789 0.963148593902588 0.588746011257172 0.692066550254822 0.751977026462555 0.68085777759552 0.954908907413483 1.00084149837494 0.981854736804962 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 4
0.7744 0
diff-high-values: (0.00255919783376157 0.0010033113649115 0.00106657086871564 -0.00237772101536393 0.00169637822546065 7.11891916580498e-4 0.00212934077717364 0.00194923370145261 0.00229484355077147 6.56086718663573e-4 0.00835348293185234) diff-low-values: (-0.887997210025787 -0.79390150308609 -1.18933153152466 -1.06666219234467 -0.988452911376953 -0.759092628955841 -0.748683929443359 -0.650666356086731 -0.90451979637146 -0.545242130756378)
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 45 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.014 seconds for contour map
INFO:: 0.065 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.019 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.014 seconds for contour map
INFO:: 0.064 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.5
INFO grid sampling...Nuvw = ( 180, 216, 108)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0.045 seconds to initialize map
INFO:: 0.05 seconds for FFT
INFO:: 0.009 seconds for statistics
Map mean: ........ 1.146e-09
Map sigma: ....... 0.3115
Map maximum: ..... 3.071
Map minimum: ..... -0.8775
INFO:: 0.051 seconds for contour map
INFO:: 0.183 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: -4.278e-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 7837
-0.3442 17839
-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 0
3.023 1
Map statistics: mean: 4.288e-07 st.d: 0.001069
Map statistics: min: -0.006856, max: 0.01192
-0.006622 5
-0.006152 21
-0.005683 31
-0.005213 53
-0.004744 114
-0.004274 221
-0.003804 460
-0.003335 817
-0.002865 1522
-0.002396 2764
-0.001926 4797
-0.001457 9242
-0.0009873 19273
-0.0005178 40373
-4.831e-05 61229
0.0004212 44297
0.0008907 20929
0.00136 9475
0.00183 4785
0.002299 2778
0.002769 1678
0.003238 1172
0.003708 689
0.004177 491
0.004647 288
0.005116 198
0.005586 151
0.006055 102
0.006525 56
0.006995 37
0.007464 18
0.007934 10
0.008403 10
0.008873 3
0.009342 1
0.009812 3
0.01028 2
0.01075 0
0.01122 0
0.01169 0
0.01216 1
INFO:: Reading coordinate file: /home/paule/data/greg-data/multi-carbo-coot-3.pdb
PDB file /home/paule/data/greg-data/multi-carbo-coot-3.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 51 read successfully
DEBUG:: there were 2 types with no dictionary
created 46 bond restraints
created 82 angle restraints
created 2 plane restraints
created 8 chiral vol restraints
created 138 restraints
INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A
INFO:: glycosidic_linkage type :ALPHA1-4:
DEBUG:: find_link_type_complicado() find_glycosidic_linkage_type() returns "ALPHA1-4"
Link restraints:
1 bond links
3 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 750 non-bonded restraints
initial distortion_score: 2652
Initial RMS Z values
bonds: 6.162
angles: 2.853
torsions: N/A
planes: 0.08353
non-bonded: 0.2254
chiral vol: 0.9035
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 887) at 15.99
Final Estimated RMS Z Scores:
bonds: 0.1009
angles: 0.4225
torsions: N/A
planes: 0.0264
non-bonded: 0.0001898
chiral vol: 0.1561
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 7.479
Removing idle function -1
debug:: restraints results 1 5
INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-3.pdb_Mon_May_14_11:46:33_2018_modification_0.pdb.gz
INFO:: replace_coords: 46 atoms updated.
PASS: Mask and difference map
Entered testcase - Skeletonize a map
PASS: Skeletonize a map
Entered testcase - Simple Averaged maps
INFO:: map sigmas: normal 0.311072021722794 and diff-map: 0.00106883328408003
PASS: Simple Averaged maps
Entered testcase - Make a glycosidic linkage
bond-length: 2.2472998823295:
bond-length: 1.44437928674295:
bond-length-within-tolerance? bond-length 1.44437928674295 with target 1.439 and tolerance 0.04 for atom ((" O4 " "") (1.0 20.0 " O" "") (-3.95734977722168 20.753511428833 1.51749432086945)) is ((" C1 " "") (1.0 20.0 " C" "") (-3.19250345230103 21.6129570007324 2.39076113700867))
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb
PDB file /home/paule/data/greg-data/pdb2qc1-sans-cho.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 3 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
INFO:: NCS chain comparison 4/110
Molecule 52 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.019 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.015 seconds for contour map
INFO:: 0.065 seconds in total
......... checking for /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab
..that failed - trying /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/NAG-decorations.tab
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Mon_May_14_11:46:33_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Mon_May_14_11:46:33_2018_modification_1.pdb.gz
INFO:: link torsion generated from link bond restraint
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Mon_May_14_11:46:33_2018_modification_2.pdb.gz
INFO:: replace_coords: 22 atoms updated.
INFO:: created 55 restraints
created 21 bond restraints
created 27 angle restraints
created 2 plane restraints
created 5 chiral vol restraints
Link restraints:
1 bond links
2 angle links
1 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 678 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 6.741e+04
Initial RMS Z values
bonds: 0.3607
angles: 0.6064
torsions: N/A
planes: 0.6834
non-bonded: 100.8
chiral vol: 0.4449
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 24) at -625.7
Final Estimated RMS Z Scores:
bonds: 2.347
angles: 2.047
torsions: N/A
planes: 1.18
non-bonded: 0.05894
chiral vol: 1.102
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 8.668
Removing idle function -1
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Mon_May_14_11:46:33_2018_modification_3.pdb.gz
INFO:: replace_coords: 22 atoms updated.
INFO:: created 55 restraints
created 21 bond restraints
created 27 angle restraints
created 2 plane restraints
created 5 chiral vol restraints
Link restraints:
1 bond links
2 angle links
1 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 451 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 1691
Initial RMS Z values
bonds: 2.347
angles: 2.047
torsions: N/A
planes: 1.18
non-bonded: 5.225
chiral vol: 1.102
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 64) at -889.4
Final Estimated RMS Z Scores:
bonds: 2.249
angles: 2.276
torsions: N/A
planes: 1.31
non-bonded: 0.1676
chiral vol: 2.338
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 8.765
Removing idle function -1
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb2qc1-sans-cho.pdb_Mon_May_14_11:46:33_2018_modification_4.pdb.gz
INFO:: replace_coords: 22 atoms updated.
PASS: Make a glycosidic linkage
Entered testcase - Refine an NAG-ASN Link
bond-length-within-tolerance? bond-length 1.58424499615156 with target 1.43 and tolerance 0.2 for atom ((" ND2" "") (1.0 16.9300003051758 " N" "") (-14.7770776748657 -0.202667862176895 -7.32550954818726)) is ((" C1 " "") (1.0 45.0 " C" "") (-13.4611644744873 -0.681442499160767 -6.58457803726196))
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-VAL.pdb
PDB file /home/paule/data/greg-data/monomer-VAL.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 54 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: found bad VAL chiral atom: A 1 CB
created 14 bond restraints
created 25 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 40 restraints
INFO:: make_restraints(): made 44 non-bonded restraints
initial distortion_score: 4.997
Initial RMS Z values
bonds: 0.5425
angles: 0.1641
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.4516
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 70) at 0.2482
Final Estimated RMS Z Scores:
bonds: 0.01222
angles: 0.09486
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.1454
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 9.055
Removing idle function -1
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_May_14_11:46:34_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: undo molecule number set to: 54
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_May_14_11:46:34_2018_modification_1.pdb.gz
restoring from backup 2 2
INFO:: Reading coordinate file: coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_May_14_11:46:34_2018_modification_0.pdb.gz
PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_May_14_11:46:34_2018_modification_0.pdb.gz has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 70) at 0.2482
Final Estimated RMS Z Scores:
bonds: 0.01222
angles: 0.09486
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.1454
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 9.128
Removing idle function -1
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_May_14_11:46:34_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
PASS: Refine an NAG-ASN Link
Entered testcase - Test for flying hydrogens on undo
bond-length-within-tolerance? bond-length 0.960061691781605 with target 0.96 and tolerance 0.02 for atom (("HG11" "") (1.0 20.0 " H" "") (3.4704897403717 -0.190908700227737 -1.96913886070251)) is ((" CG1" "") (1.0 20.0 " C" "") (2.87013721466064 -0.207151547074318 -1.22011852264404))
INFO:: Reading coordinate file: /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb
PDB file /home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 55 read successfully
DEBUG:: there were 0 types with no dictionary
created 17 bond restraints
created 31 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 49 restraints
INFO:: make_restraints(): made 67 non-bonded restraints
initial distortion_score: 903.1
Initial RMS Z values
bonds: 5.621
angles: 3.433
torsions: N/A
planes: N/A
non-bonded: 0
chiral vol: 0.7534
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 165) at 0.4747
Final Estimated RMS Z Scores:
bonds: 0.009429
angles: 0.121
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): 9.467
Removing idle function -1
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Mon_May_14_11:46:35_2018_modification_0.pdb.gz
INFO:: replace_coords: 18 atoms updated.
PASS: Test for flying hydrogens on undo
Entered testcase - Test for regularization and mangling of hydrogen names from a PDB v 3.0
bond-length-within-tolerance? bond-length 0.959993508181978 with target 0.96 and tolerance 0.02 for atom (("HD11" "") (1.0 10.5299997329712 " H" "") (-10.1156616210938 6.52059507369995 7.01407289505005)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977))
bond-length-within-tolerance? bond-length 0.96002780270247 with target 0.96 and tolerance 0.02 for atom (("HD12" "") (1.0 10.1300001144409 " H" "") (-9.7598762512207 5.68341684341431 5.73144054412842)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977))
bond-length-within-tolerance? bond-length 0.959946651623676 with target 0.96 and tolerance 0.02 for atom (("HD13" "") (1.0 10.5600004196167 " H" "") (-11.027907371521 5.31390428543091 6.58492517471313)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1280078887939 5.64651441574097 6.61731338500977))
bond-length-within-tolerance? bond-length 0.959995371308682 with target 0.96 and tolerance 0.02 for atom (("HD21" "") (1.0 10.1499996185303 " H" "") (-7.9939432144165 3.15288591384888 7.14437961578369)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627))
bond-length-within-tolerance? bond-length 0.960016201142166 with target 0.96 and tolerance 0.02 for atom (("HD22" "") (1.0 10.3000001907349 " H" "") (-9.20783233642578 3.14652538299561 6.14453363418579)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627))
bond-length-within-tolerance? bond-length 0.959897847605806 with target 0.96 and tolerance 0.02 for atom (("HD23" "") (1.0 10.6499996185303 " H" "") (-8.02846336364746 4.16698122024536 5.94336414337158)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55896663665771 3.69613480567932 6.5901050567627))
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: 2010
Initial RMS Z values
bonds: 1.152
angles: 0.8476
torsions: N/A
planes: 3.056
non-bonded: 81.91
chiral vol: 0.7578
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 20) at -1124
Final Estimated RMS Z Scores:
bonds: 0.8539
angles: 0.5551
torsions: N/A
planes: 0.5105
non-bonded: 0.08573
chiral vol: 0.1709
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 9.52
Removing idle function -1
Refinement elapsed time: 0.008
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:35_2018_modification_0.pdb.gz
INFO:: replace_coords: 12 atoms updated.
PASS: Test for regularization and 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: 2.60342967060332:
bond-length-within-tolerance? bond-length 2.60342967060332 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.2833099365234 4.44525146484375 19.7411441802979)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.5063095092773 6.64316701889038 19.0693664550781))
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: 1334
Initial RMS Z values
bonds: 14.34
angles: 0.5551
torsions: N/A
planes: 0.5105
non-bonded: 0
chiral vol: 0.1709
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 49) at -1220
Final Estimated RMS Z Scores:
bonds: 0.2885
angles: 0.3375
torsions: N/A
planes: 0.7811
non-bonded: 0
chiral vol: 0.2558
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 9.542
Removing idle function -1
Refinement elapsed time: 0.009
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:35_2018_modification_1.pdb.gz
INFO:: replace_coords: 12 atoms updated.
pass intermediate 2.8 tolerance test
OK plane atom " CB "
Bond-length: 1.51943200610776:
bond-length-within-tolerance? bond-length 1.51943200610776 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5516204833984 4.88503265380859 19.3988819122314)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.3084411621094 6.16733884811401 19.096248626709))
INFO:: wrote mmCIF "coot-test-ala.cif"
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb
PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 57 read successfully
DEBUG:: there were 1 types with no dictionary
Welcome to Coot
WARNING:: bond_restraint_length 4 should be 5
created 5 bond restraints
created 9 angle restraints
created 1 plane restraints
created 0 chiral vol restraints
created 15 restraints
INFO:: make_restraints(): made 7 non-bonded restraints
initial distortion_score: 4849
Initial RMS Z values
bonds: 0.01199
angles: 0.00654
torsions: N/A
planes: 0
non-bonded: 689.9
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 71) at -300.3
Final Estimated RMS Z Scores:
bonds: 0.05342
angles: 0.4146
torsions: N/A
planes: 0.05545
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 9.925
Removing idle function -1
Refinement elapsed time: 0.015
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Mon_May_14_11:46:35_2018_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 58 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_1.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 26 A 27
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_2.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_3.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_5.pdb.gz
INFO:: Removing CIS peptide from PDB header: B 26 B 27
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_6.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_7.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 59 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_1.pdb.gz
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)
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:36_2018_modification_0.pdb.gz
INFO:: replace_coords: 1465 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 62 read successfully
DEBUG:: there were 0 types with no dictionary
in new_molecule_by_residue_type_selection Something bad happened - No residues selected
in new_molecule_by_residue_type_selection Something bad happened - No residues selected
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:37_2018_modification_0.pdb.gz
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 63 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%]
INFO:: Reading coordinate file: /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb
PDB file /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 50/87
Molecule 64 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: aligning to mol number 64 chain: A
----- input to align_on_chain() -----------------
chain A
target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
wgap -3
is_nucleic_acid_flag 0
console_output 1
---------------------------------------------------
INFO:: input model sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID
INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
> /home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb
> target sequence:
---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID
||||||| |||||||||| ||||||| ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||
DVSGTVCLSALPPEATDTLNLIAS-DGPFPYSQ-DGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
INFO:: alignment score 150
DEBUG:: s.length() 95
DEBUG:: nSelResidues 87
INFO:: backup file coot-backup/_home_paule_data_greg-data_rnase-A-needs-an-insertion.pdb_Mon_May_14_11:46:37_2018_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: 108735976 "A" 1 ""] -> ASP
[spec: 108735976 "A" 2 ""] -> VAL
[spec: 108735976 "A" 3 ""] -> SER
[spec: 108735976 "A" 11 ""] -> LEU
[spec: 108735976 "A" 12 ""] -> PRO
[spec: 108735976 "A" 13 ""] -> PRO
[spec: 108735976 "A" 62 ""] -> PRO
[spec: 108735976 "A" 63 ""] -> GLY
Deletions:
[spec: 108735976 "A" 25 ""]
[spec: 108735976 "A" 34 ""]
Mutations:
[spec: 108735976 "A" 24 ""] -> SER
[spec: 108735976 "A" 33 ""] -> GLN
INFO:: mutate 24 A to a SER
INFO:: mutate 33 A to a GLN
apply resno updates...
Applied 3 insertions
Applied 2 mutations
Applied 2 deletions
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 65 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:37_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 66 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:38_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb3hfl.ent
PDB file /home/paule/data/greg-data/pdb3hfl.ent has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 15/212
INFO:: NCS chain comparison 7/212
INFO:: NCS chain comparison 10/215
Molecule 67 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz
Number of OBSERVED reflections: 17920
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 64, 96, 90)
INFO:: 0.022 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: ........ 7.462e-11
Map sigma: ....... 0.2604
Map maximum: ..... 1.718
Map minimum: ..... -1.034
INFO:: 0.006 seconds for contour map
INFO:: 0.044 seconds in total
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_May_14_11:46:38_2018_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Fitting score for best rotamer: 5.834
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_May_14_11:46:38_2018_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
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 0/8
INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_May_14_11:46:38_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_May_14_11:46:38_2018_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
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 0/8
INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_May_14_11:46:38_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_May_14_11:46:38_2018_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
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 0/8
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_May_14_11:46:38_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_May_14_11:46:38_2018_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_Mon_May_14_11:46:38_2018_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_Mon_May_14_11:46:38_2018_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_Mon_May_14_11:46:38_2018_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
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 0/8
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_May_14_11:46:38_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_May_14_11:46:38_2018_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_Mon_May_14_11:46:38_2018_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_Mon_May_14_11:46:38_2018_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_Mon_May_14_11:46:38_2018_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:: mutate 32 A to a LYS
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:38_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/some-waters-with-ter.pdb
PDB file /home/paule/data/greg-data/some-waters-with-ter.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 74 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_some-waters-with-ter.pdb_Mon_May_14_11:46:39_2018_modification_0.pdb.gz
1/D/79 {HOH}/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule
INFO:: Reading coordinate file: /home/paule/data/greg-data/tm+some-waters.pdb
PDB file /home/paule/data/greg-data/tm+some-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 75 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Protein centre at: xyz = ( 41.57, 8.745, 12.89)
using sigma cut off 2
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.3115
INFO:: Using density cut-off: 0.623 (2 sigma) (mean -0.0337 stdev: 0.1461)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
-------------------------------------------------------------
INFO:: cluster at xyz = ( 59.91, 3.027, -4.296) is too big to be water
INFO:: cluster at xyz = ( 70.01, 19.05, 18.63) is too big to be water
INFO:: found 45 waters in water fitting
Done - back from lig.water_fit()
DEBUG:: new_waters_mol_flag: 0
INFO:: backup file coot-backup/_home_paule_data_greg-data_tm+some-waters.pdb_Mon_May_14_11:46:39_2018_modification_0.pdb.gz
INFO:: Adding to solvent chain: D
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 76 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_0.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_1.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_2.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_3.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_4.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_5.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_6.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_7.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_8.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_9.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_10.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_11.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_12.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_13.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_14.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_15.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_16.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_17.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_18.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_19.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_20.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_21.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_22.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_23.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_24.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_25.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_26.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_27.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_28.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_29.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_30.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_31.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_32.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_33.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_34.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_35.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_36.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_37.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_38.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_39.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_40.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_41.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_42.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_43.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_44.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_45.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_46.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_47.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_48.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_49.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_50.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_51.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_52.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_53.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_54.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_55.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_56.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_57.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_58.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_59.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_60.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_61.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_62.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_63.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_64.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_65.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_66.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_67.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_68.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_69.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_70.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_71.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_72.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_73.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_74.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_75.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_76.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_77.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_78.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_79.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_80.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_81.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_82.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_83.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_84.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_85.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_86.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_87.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_88.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_89.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_90.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_91.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_92.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_93.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_94.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_95.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_96.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_97.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_98.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:39_2018_modification_99.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: Reading coordinate file: /home/paule/data/greg-data/water-test-no-cell.pdb
PDB file /home/paule/data/greg-data/water-test-no-cell.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 77 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_water-test-no-cell.pdb_Mon_May_14_11:46:42_2018_modification_0.pdb.gz
No symmetry available
INFO:: moved 0 water molecules
INFO:: Reading coordinate file: /home/paule/data/greg-data/pathological-water-test.pdb
PDB file /home/paule/data/greg-data/pathological-water-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 78 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_pathological-water-test.pdb_Mon_May_14_11:46:43_2018_modification_0.pdb.gz
INFO:: moved 181 water molecules
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.03 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.019 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.014 seconds for contour map
INFO:: 0.067 seconds in total
fitting terminal residue with 1000 random trials
called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:43_2018_modification_0.pdb.gz
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)
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: 81 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 81 and ichain: 0
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 0
Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 93/93
First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.88,12.96,8.761) B-factor: 30.17
First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.88,16.17,23.03) B-factor: 20.03
INFO:: LSQ matched 93 atoms
INFO:: 93 matched atoms had:
mean devi: 1.179
rms devi: 4.859
max devi: 46.26
min devi: 0.1254
find_ncs_matrix returns (LSQ)
| 0.9637, -0.07462, -0.2563|
| 0.2651, 0.3804, 0.886|
| 0.0314, -0.9218, 0.3864|
( 38.09, -17.87, 14.32)
Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:43_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 82 read successfully
DEBUG:: there were 0 types with no dictionary
0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.6,8.687,12.91) B-factor: 45 added to molecule (and new chain)
1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.6,8.687,12.91) B-factor: 45 added to molecule
1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.6,8.687,12.91) B-factor: 45 added to molecule
1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.6,8.687,12.91) B-factor: 45 added to molecule
1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.6,8.687,12.91) B-factor: 45 added to molecule
1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.6,8.687,12.91) B-factor: 45 added to molecule
1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.6,8.687,12.91) B-factor: 45 added to molecule
1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.6,8.687,12.91) B-factor: 45 added to molecule
1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.6,8.687,12.91) B-factor: 45 added to molecule
1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.6,8.687,12.91) B-factor: 45 added to molecule
1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.6,8.687,12.91) B-factor: 45 added to molecule
1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.6,8.687,12.91) B-factor: 45 added to molecule
1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.6,8.687,12.91) B-factor: 45 added to molecule
1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.6,8.687,12.91) B-factor: 45 added to molecule
1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.6,8.687,12.91) B-factor: 45 added to molecule
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent
PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
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 83 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-ACT.pdb
PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 84 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb
PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 85 read successfully
DEBUG:: there were 1 types with no dictionary
-X,-X+Y,-Z+1/3 ->
-1 0 0
-1 1 0
0 0 -1
translations: 0 0 0.3333
pre-trans: 0 0 0
INFO:: NCS chain comparison 62/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.57,-20.5,95.47) B-factor: 45.26
First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (64.42,-37.85,121.4) B-factor: 88.52
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had:
mean devi: 2.499
rms devi: 2.796
max devi: 6.686
min devi: 0.4401
find_ncs_matrix returns (LSQ)
| 0.8045, 0.069, 0.59|
| 0.5435, 0.315, -0.778|
| -0.2395, 0.9466, 0.2159|
( -57.32, 43.57, 131.4)
INFO:: NCS chain comparison 66/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.57,-20.5,95.47) B-factor: 45.26
First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (-18.26,-63.04,111.4) B-factor: 50.76
INFO:: LSQ matched 66 atoms
INFO:: 66 matched atoms had:
mean devi: 1.971
rms devi: 2.173
max devi: 4.541
min devi: 0.4295
find_ncs_matrix returns (LSQ)
| -0.5596, -0.8266, 0.06065|
| -0.8239, 0.5468, -0.1492|
| 0.09015, -0.1334, -0.9869|
( -4.436, 16.92, 204.3)
INFO:: NCS chain comparison 61/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (62.57,-20.5,95.47) B-factor: 45.26
First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (-0.2911,-72.48,94.47) B-factor: 78.35
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had:
mean devi: 3.704
rms devi: 4.086
max devi: 9.438
min devi: 0.2858
find_ncs_matrix returns (LSQ)
| -0.4782, -0.7381, -0.476|
| -0.7473, 0.05733, 0.662|
| -0.4613, 0.6723, -0.579|
( 53.45, -87.51, 210.2)
INFO:: NCS chain comparison 0/67
INFO:: NCS chain comparison 0/67
INFO:: NCS chain comparison 0/54
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:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 87 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:45_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:45_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_May_14_11:46:45_2018_modification_1.pdb.gz
INFO:: Matching/moving molecule number 90 to 89
INFO:: LSQ matched 4 atoms
INFO:: 4 matched atoms had:
mean devi: 0.03532
rms devi: 0.03779
max devi: 0.05453
min devi: 0.01668
INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076)
INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313)
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:45_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| 0.9737, 0.007115, -0.2278|
| 0.2062, 0.3981, 0.8939|
| 0.09703, -0.9173, 0.3861|
( 37.45, -16.6, 12.88)
INFO:: fractional coordinates matrix:
| 0.9737, 0.008587, -0.1361|
| 0.1708, 0.3981, 0.4427|
| 0.1623, -1.852, 0.3861|
( 0.577, -0.2119, 0.3319)
PASS: update monomer restraints
Entered testcase - Write mmCIF restraints correctly
PASS: Write mmCIF restraints correctly
Entered testcase - Refinement OK with zero bond esd
PASS: Refinement OK with zero bond esd
Entered testcase - Change Chain IDs and Chain Sorting
PASS: Change Chain IDs and Chain Sorting
Entered testcase - Chain-ids in links change also on change chain id
PASS: Chain-ids in links change also on change chain id
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
::::: (64 "A" 1 "") #f #f
::::: (64 "A" 4 "") #t #t
::::: (64 "A" 57 "") #t #t
::::: (64 "A" 60 "") #f #f
::::: (64 "A" 61 "") #f #f
::::: (64 "A" 92 "") #t #t
::::: (64 "A" 94 "") #f #f
results: (#t #t #t #t #t #t #t)
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 - Test for good chain ids after a merge
chain-ids: ("AAA" "B" "B-chain")
--- chain-ids: ("AAA" "B" "B-chain" "AAA_2")
PASS: Test for good chain ids after a merge
Entered testcase - LSQ by atom
bond-length-within-tolerance? bond-length 0.110921496735531 with target 0.0 and tolerance 0.2 for atom ((" C " "") (1.0 15.5799999237061 " C" "") (56.8940010070801 1.29299998283386 19.6700000762939)) is ((" C " "") (1.0 16.7800006866455 " C" "") (56.8856086730957 1.18242847919464 19.6726627349854))
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 91 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1py3.ent
PDB file /home/paule/data/greg-data/pdb1py3.ent has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
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 92 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: spacegroup: P 21 21 21
INFO:: spacegroup: C 1 2 1
INFO:: Matching/moving molecule number 91 to 92
INFO:: LSQ matched 164 atoms
INFO:: 164 matched atoms had:
mean devi: 0.5023
rms devi: 0.5938
max devi: 1.679
min devi: 0.04318
INFO:: Axis orientation: ( 0.567, -0.7175, 0.4046)
INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019)
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:45_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| 0.8273, 0.1661, 0.5366|
| -0.3732, 0.8765, 0.3041|
| -0.4199, -0.4519, 0.7871|
( 33.77, -3.902, -16.53)
INFO:: fractional coordinates matrix:
| 0.8273, 0.2005, 0.3208|
| -0.3092, 0.8765, 0.1506|
| -0.7024, -0.9123, 0.7871|
( 0.5204, -0.04982, -0.426)
INFO:: spacegroup: C 1 2 1
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 93 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:46_2018_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 94 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/2goz-manip.pdb
PDB file /home/paule/data/greg-data/2goz-manip.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 7 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
INFO:: NCS chain comparison 10/85
Molecule 95 read successfully
DEBUG:: there were 7 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 96 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.021 seconds for FFT
INFO:: 0.003 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.015 seconds for contour map
INFO:: 0.067 seconds in total
masking....masking done
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:46:47_2018_modification_0.pdb.gz
INFO:: replace_coords: 745 atoms updated.
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:: read_file() chain with chain id has 2 residues
Symmetry available for this molecule
Molecule 98 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:: read_file() chain with chain id has 2 residues
Symmetry available for this molecule
Molecule 99 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:: read_file() chain with chain id has 121 residues
Symmetry available for this molecule
Molecule 100 read successfully
Map statistics: mean: -5.07e-05 st.d: 0.3052
Map statistics: min: -0.781, max: 6.079
-0.6953 231
-0.5238 4724
-0.3523 24910
-0.1808 55291
-0.00927 95241
0.1622 40930
0.3337 7480
0.5052 3968
0.6767 2790
0.8482 2117
1.02 1738
1.191 1221
1.363 888
1.534 595
1.706 355
1.877 240
2.049 137
2.22 97
2.392 62
2.563 46
2.735 17
2.906 17
3.078 13
3.249 10
3.421 7
3.592 1
3.764 3
3.935 7
4.107 2
4.278 5
4.45 1
4.621 2
4.793 2
4.964 0
5.136 1
5.307 0
5.479 0
5.65 0
5.822 0
5.993 1
6.165 0
Map statistics: mean: -1.005e-05 st.d: 0.04681
Map statistics: min: -0.2115, max: 0.6486
-0.2008 7
-0.1793 48
-0.1578 209
-0.1363 787
-0.1148 2257
-0.09325 5676
-0.07175 12730
-0.05025 24380
-0.02874 38190
-0.007239 46230
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.
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 ((94 "A" 1 "") (94 "A" 2 "") (94 "A" 3 "") (94 "A" 4 "") (94 "A" 5 "") (94 "A" 6 "") (94 "A" 7 "") (94 "A" 8 "") (94 "A" 9 "") (94 "A" 10 "") (94 "A" 11 "") (94 "A" 12 "") (94 "A" 13 "") (94 "A" 14 "") (94 "A" 15 "") (94 "A" 16 "") (94 "A" 17 "") (94 "A" 18 "") (94 "A" 19 "") (94 "A" 20 "") (94 "A" 21 "") (94 "A" 22 "") (94 "A" 23 "") (94 "A" 24 "") (94 "A" 25 "") (94 "A" 26 "") (94 "A" 27 "") (94 "A" 28 "") (94 "A" 29 "") (94 "A" 30 "") (94 "A" 31 "") (94 "A" 32 "") (94 "A" 33 "") (94 "A" 34 "") (94 "A" 35 "") (94 "A" 36 "") (94 "A" 37 "") (94 "A" 38 "") (94 "A" 39 "") (94 "A" 40 "") (94 "A" 41 "") (94 "A" 42 "") (94 "A" 43 "") (94 "A" 44 "") (94 "A" 45 "") (94 "A" 46 "") (94 "A" 47 "") (94 "A" 48 "") (94 "A" 49 "") (94 "A" 50 "") (94 "A" 51 "") (94 "A" 52 "") (94 "A" 53 "") (94 "A" 54 "") (94 "A" 55 "") (94 "A" 56 "") (94 "A" 57 "") (94 "A" 58 "") (94 "A" 59 "") (94 "A" 60 "") (94 "A" 61 "") (94 "A" 62 "") (94 "A" 63 "") (94 "A" 64 "") (94 "A" 65 "") (94 "A" 66 "") (94 "A" 67 "") (94 "A" 68 "") (94 "A" 69 "") (94 "A" 70 "") (94 "A" 71 "") (94 "A" 72 "") (94 "A" 73 "") (94 "A" 74 "") (94 "A" 75 "") (94 "A" 76 "") (94 "A" 77 "") (94 "A" 78 "") (94 "A" 79 "") (94 "A" 80 "") (94 "A" 81 "") (94 "A" 82 "") (94 "A" 83 "") (94 "A" 84 "") (94 "A" 85 "") (94 "A" 86 "") (94 "A" 87 "") (94 "A" 88 "") (94 "A" 89 "") (94 "A" 90 "") (94 "A" 91 "") (94 "A" 92 "") (94 "A" 93 "") (94 "B" 1 "") (94 "B" 2 "") (94 "B" 3 "") (94 "B" 4 "") (94 "B" 5 "") (94 "B" 6 "") (94 "B" 7 "") (94 "B" 8 "") (94 "B" 9 "") (94 "B" 10 "") (94 "B" 11 "") (94 "B" 12 "") (94 "B" 13 "") (94 "B" 14 "") (94 "B" 15 "") (94 "B" 16 "") (94 "B" 17 "") (94 "B" 18 "") (94 "B" 19 "") (94 "B" 20 "") (94 "B" 21 "") (94 "B" 22 "") (94 "B" 23 "") (94 "B" 24 "") (94 "B" 25 "") (94 "B" 26 "") (94 "B" 27 "") (94 "B" 28 "") (94 "B" 29 "") (94 "B" 30 "") (94 "B" 31 "") (94 "B" 32 "") (94 "B" 33 "") (94 "B" 34 "") (94 "B" 35 "") (94 "B" 36 "") (94 "B" 37 "") (94 "B" 38 "") (94 "B" 39 "") (94 "B" 40 "") (94 "B" 41 "") (94 "B" 42 "") (94 "B" 43 "") (94 "B" 44 "") (94 "B" 45 "") (94 "B" 46 "") (94 "B" 47 "") (94 "B" 48 "") (94 "B" 49 "") (94 "B" 50 "") (94 "B" 51 "") (94 "B" 52 "") (94 "B" 53 "") (94 "B" 54 "") (94 "B" 55 "") (94 "B" 56 "") (94 "B" 57 "") (94 "B" 58 "") (94 "B" 59 "") (94 "B" 60 "") (94 "B" 61 "") (94 "B" 62 "") (94 "B" 63 "") (94 "B" 64 "") (94 "B" 65 "") (94 "B" 66 "") (94 "B" 67 "") (94 "B" 68 "") (94 "B" 69 "") (94 "B" 70 "") (94 "B" 71 "") (94 "B" 72 "") (94 "B" 73 "") (94 "B" 74 "") (94 "B" 75 "") (94 "B" 76 "") (94 "B" 77 "") (94 "B" 78 "") (94 "B" 79 "") (94 "B" 80 "") (94 "B" 81 "") (94 "B" 82 "") (94 "B" 83 "") (94 "B" 84 "") (94 "B" 85 "") (94 "B" 86 "") (94 "B" 87 "") (94 "B" 88 "") (94 "B" 89 "") (94 "B" 90 "") (94 "B" 91 "") (94 "B" 92 "") (94 "B" 93 "") (94 "B" 94 "") (94 "B" 95 "") (94 "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
Entered testcase - Fix for Oliver Clarke fit by atom selection bug
bl: 0.0363726829001203
PASS: Fix for Oliver Clarke fit by atom selection bug
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 mfitting terminal residue with 1000 random trials
called fit_terminal_residue_generic() residue-seqnum: 2020 offset: 1
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/atom_selection_from_insulin.res_Mon_May_14_11:46:48_2018_modification_0.res
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " N "
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CA "
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " C "
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " O "
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CB "
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CG "
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " ND1"
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CE1"
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " NE2"
WARNING:: failed to get AFIX handle for "B" 2010 "HIS" " CD2"
INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Mon_May_14_11:46:48_2018_modification_0.res
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N "
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA "
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C "
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2"
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1"
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1"
1/D/3069 {HOH}/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule
INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56)
using sigma cut off 0.6
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.3052
INFO:: Using density cut-off: 0.1831 (0.6 sigma) (mean -0.02035 stdev: 0.1119)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
-------------------------------------------------------------
INFO:: cluster at xyz = ( -4.859, 20.8, 69.7) is too big to be water
INFO:: cluster at xyz = ( 4.249, -1.354, 48.69) is too big to be water
INFO:: cluster at xyz = ( 0.05491, 16.3, 69.67) is too big to be water
INFO:: cluster at xyz = ( 15.59, 8.13, 53.24) is too big to be water
INFO:: cluster at xyz = ( 20.55, 4.875, 65.84) is too big to be water
INFO:: cluster at xyz = ( -5.054, 9.822, 69.12) is too big to be water
INFO:: found 28 waters in water fitting
Done - back from lig.water_fit()
DEBUG:: new_waters_mol_flag: 0
INFO:: backup file coot-backup/_home_paule_data_greg-data_insulin.res_Mon_May_14_11:46:48_2018_modification_1.res
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " N "
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " CA "
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " C "
WARNING:: failed to get AFIX handle for "A" 1001 "GLY" " O "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " N "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CA "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CB "
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG2"
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CG1"
WARNING:: failed to get AFIX handle for "A" 1002 "ILE" " CD1"
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:: read_file() chain with chain id has 5 residues
Symmetry available for this molecule
Molecule 105 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:: read_file() chain with chain id has 23 residues
Symmetry available for this molecule
Molecule 106 read successfully
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C1 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " O1 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C2 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C3 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H3 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C4 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " H4 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " C5 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" "CL1 "
WARNING:: failed to get AFIX handle for "A" 1 "CPC" " N1 "
INFO:: SHELXL file new-horma.ins written.
LATT LINE: LATT -1
SFAC LINE: SFAC C H N O MG CL
debug:: ## new chain wiith chain-id A
INFO:: CELL set to 14.08 32.76 18.66 90 101.7 90
READ-INS:: Spacegroup: "P 1 21 1"
INFO:: read_file() chain with chain id A has 23 residues
Symmetry available for this molecule
Molecule 107 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:: read_file() chain with chain id has 4 residues
Symmetry available for this molecule
Molecule 108 read successfully
INFO:: Creating directory coot-ccp4
olecule 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 5.2.01 ; 10.04.2013/
:
:
: 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 5.41
: _lib_update 11/02/13
: ------------------------------
: NUMBER OF MONOMERS IN THE LIBRARY : 11471
: with complete description : 11471
: NUMBER OF MODIFICATIONS : 59
: NUMBER OF LINKS : 70
: 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 6.4: Refmac_5.8.0073 version 5.8.0073 : 25/05/14##
: ###############################################################
: User: unknown Run date: 14/ 5/2018 Run time: 11:46:50
:
:
: Please reference: Collaborative Computational Project, Number 4. 1994.
: "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
: as well as any specific reference in the program write-up.
:
:<!--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
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
:
: **** Input and Default parameters# ****
:
:
:Input coordinate file. Logical name - XYZIN actual file name - coot-ccp4/libcheck_3GP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name - coot-ccp4/monomer-3GP.pdb
:
: Refinement type : Idealisation
:
: **** Makecif parameters ****
:
:Dictionary files for restraints : /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/ener_lib.cif
:User supplied dictionary entries: coot-ccp4/libcheck_3GP.cif
: Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
: Hydrogens will be restored in their riding positions
: hydrogens will be written to the output file
: Links between monomers will be checked. Only those links present in the coordinate file will be used
: Standard sugar links will be analysed and used
: For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
: Symmetry related links will be analysed and used
: Cis peptides will be found and used automatically
:
:
:
:
:Monitoring style is "MEDIUM". Complete information will be printed out in the
:first and last cycle. In all other cycles minimum information will be printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will be printed out
:Distance outliers 10.000
:Angle outliers 10.000
:Torsion outliers 10.000
:Chiral volume outliers 10.000
:Plane outliers 10.000
:Non-bonding outliers 10.000
:---------------------------------------------------------------
:
: Input file :coot-ccp4/libcheck_3GP.pdb
: ------------------------------
: --- LIBRARY OF MONOMERS ---
: _lib_name mon_lib
: _lib_version 5.41
: _lib_update 11/02/13
: ------------------------------
: NUMBER OF MONOMERS IN THE LIBRARY : 11471
: with complete description : 11471
: NUMBER OF MODIFICATIONS : 59
: NUMBER OF LINKS : 70
: 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: /home/paule/ccp4/ccp4-6.4.0/lib/data/atomsf.lib
:<!--SUMMARY_END--></FONT></B>
:
:
: Spacegroup information obtained from library file:
: Logical Name: SYMINFO Filename: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/syminfo.lib
:
: WARNING: "SCALE" card is absent in input PDB file
: Number of atoms : 36
: Number of residues : 1
: Number of chains : 1
: I am reading library. Please wait.
: mon_lib.cif
: --------------------------------
: --- title of input coord file ---
:
: PDB_code:3GP
: PDB_name:coords of 3GP from prog: libcheck
: PDB_date:XX-XXX-XX
: --------------------------------
: Number of chains : 1
: Total number of monomers : 1
: Number of atoms : 36
: Number of missing atoms : 0
: Number of rebuilt atoms : 0
: Number of unknown atoms : 0
: Number of deleted atoms : 0
: pdb_in_format P
:
:
: loop_
: _atom_type_symbol
: _atom_type_scat_Cromer_Mann_a1
: _atom_type_scat_Cromer_Mann_b1
: _atom_type_scat_Cromer_Mann_a2
: _atom_type_scat_Cromer_Mann_b2
: _atom_type_scat_Cromer_Mann_a3
: _atom_type_scat_Cromer_Mann_b3
: _atom_type_scat_Cromer_Mann_a4
: _atom_type_scat_Cromer_Mann_b4
: _atom_type_scat_Cromer_Mann_c
:
:
: O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508
: C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156
: N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290
: H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030
: P 6.4345 1.9067 4.1791 27.1570 1.7800 0.5260 1.4908 68.1645 1.1149
:
:
: Number of distances : 0
: Number of angles : 0
: Number of torsions : 0
: Number of planes : 0
: Number of chirals : 0
: Number of intervals : 0
:--------------------------------------------------------------------------------
:--------------------------------------------------------------------------------
: Standard External All
: Bonds: 38 0 38
: Angles: 66 0 66
: Chirals: 4 0 4
: Planes: 2 0 2
: Torsions: 22 0 22
: Intervals: 0 0 0
:--------------------------------------------------------------------------------
:
:
: Number of harmonic restraints = 0
: Number of atoms in special position = 0
: -----------------------------------------------------
:
: chir max = 0.00000000
: chir_max = 0.00000000 3.00000000 5.00000000
:
:
: CGMAT cycle number = 1
:
: function value 88.9606705
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.030 0.020
:Bond distances: others 12 0.001 0.020
:Bond angles : refined atoms 40 4.292 3.000
:Bond angles : others 26 1.222 3.000
:Chiral centres: refined atoms 4 0.186 0.200
:Planar groups: refined atoms 14 0.002 0.020
:Planar groups: others 6 0.005 0.020
:VDW repulsions.others 6 0.189 0.200
:VDW; torsion: refined_atoms 7 0.281 0.200
:VDW; torsion.others 4 0.224 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.00000000
: Not converging with gamma equal 0.00000000
: Trying gamma equal 5.24999984E-02
: Gamma decreased to 4.19999994E-02
:
:
: fvalues 0.00000000 88.9606705 31.4238358 88.9606705
:
:
: CGMAT cycle number = 2
:
: function value 31.4238358
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.009 0.020
:Bond distances: others 12 0.002 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19999994E-02
: Gamma decreased to 3.24545428E-02
:
:
: fvalues 0.00000000 31.4238358 28.0699558 31.4238358
:
:
: CGMAT cycle number = 3
:
: function value 28.0699558
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 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 0.00000000 28.0699558 27.6102104 28.0699558
:
:
: CGMAT cycle number = 4
:
: function value 27.6102104
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.89008236E-02
: Not converging with gamma equal 6.89008236E-02
: Trying gamma equal 0.112387851
: Gamma decreased to 0.103690445
:
:
: fvalues 0.00000000 27.6102104 27.4126644 27.6102104
:
:
: CGMAT cycle number = 5
:
: function value 27.4126644
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 0.103690445
: Gamma decreased to 9.57837105E-02
:
:
: fvalues 0.00000000 27.4126644 27.2551918 27.4126644
:
:
: CGMAT cycle number = 6
:
: function value 27.2551918
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 9.57837105E-02
: Gamma decreased to 8.85957703E-02
:
:
: fvalues 0.00000000 27.2551918 27.1208076 27.2551918
:
:
: CGMAT cycle number = 7
:
: function value 27.1208076
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.85957703E-02
: Gamma decreased to 8.20612833E-02
:
:
: fvalues 0.00000000 27.1208076 26.9984283 27.1208076
:
:
: CGMAT cycle number = 8
:
: function value 26.9984283
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.20612833E-02
: Gamma decreased to 7.61208385E-02
:
:
: fvalues 0.00000000 26.9984283 26.8823528 26.9984283
:
:
: CGMAT cycle number = 9
:
: function value 26.8823528
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.61208385E-02
: Gamma decreased to 7.07204342E-02
:
:
: fvalues 0.00000000 26.8823528 26.7692947 26.8823528
:
:
: CGMAT cycle number = 10
:
: function value 26.7692947
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.07204342E-02
: Gamma decreased to 6.58109784E-02
:
:
: fvalues 0.00000000 26.7692947 26.6576500 26.7692947
:
:
: CGMAT cycle number = 11
:
: function value 26.6576500
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.58109784E-02
: Not converging with gamma equal 6.58109784E-02
: Trying gamma equal 8.92424807E-02
: Gamma decreased to 8.45561773E-02
:
:
: fvalues 0.00000000 26.6576500 26.5732040 26.6576500
:
:
: CGMAT cycle number = 12
:
: function value 26.5732040
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.45561773E-02
: Gamma decreased to 8.02959055E-02
:
:
: fvalues 0.00000000 26.5732040 26.4892159 26.5732040
:
:
: CGMAT cycle number = 13
:
: function value 26.4892159
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.02959055E-02
: Gamma decreased to 7.64229298E-02
:
:
: fvalues 0.00000000 26.4892159 26.4056892 26.4892159
:
:
: CGMAT cycle number = 14
:
: function value 26.4056892
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.64229298E-02
: Gamma decreased to 7.29020461E-02
:
:
: fvalues 0.00000000 26.4056892 26.3228664 26.4056892
:
:
: CGMAT cycle number = 15
:
: function value 26.3228664
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.29020461E-02
: Gamma decreased to 6.97012395E-02
:
:
: fvalues 0.00000000 26.3228664 26.2409363 26.3228664
:
:
: CGMAT cycle number = 16
:
: function value 26.2409363
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.97012395E-02
: Not converging with gamma equal 6.97012395E-02
: Trying gamma equal 8.49778131E-02
: Gamma decreased to 8.19225013E-02
:
:
: fvalues 0.00000000 26.2409363 26.1733379 26.2409363
:
:
: CGMAT cycle number = 17
:
: function value 26.1733379
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.19225013E-02
: Gamma decreased to 7.91449398E-02
:
:
: fvalues 0.00000000 26.1733379 26.1063652 26.1733379
:
:
: CGMAT cycle number = 18
:
: function value 26.1063652
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.91449398E-02
: Gamma decreased to 7.66198859E-02
:
:
: fvalues 0.00000000 26.1063652 26.0401402 26.1063652
:
:
: CGMAT cycle number = 19
:
: function value 26.0401402
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.66198859E-02
: Gamma decreased to 7.43243843E-02
:
:
: fvalues 0.00000000 26.0401402 25.9748650 26.0401402
:
:
: CGMAT cycle number = 20
:
: function value 25.9748650
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.43243843E-02
: Gamma decreased to 7.22375661E-02
:
:
: fvalues 0.00000000 25.9748650 25.9106178 25.9748650
:
:
: CGMAT cycle number = 21
:
: function value 25.9106178
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.22375661E-02
: Gamma decreased to 7.03404546E-02
:
:
: fvalues 0.00000000 25.9106178 25.8475819 25.9106178
:
:
: CGMAT cycle number = 22
:
: function value 25.8475819
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.03404546E-02
: Gamma decreased to 6.86158091E-02
:
:
: fvalues 0.00000000 25.8475819 25.7858162 25.8475819
:
:
: CGMAT cycle number = 23
:
: function value 25.7858162
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.86158091E-02
: Gamma decreased to 6.70479462E-02
:
:
: fvalues 0.00000000 25.7858162 25.7253666 25.7858162
:
:
: CGMAT cycle number = 24
:
: function value 25.7253666
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.70479462E-02
: Not converging with gamma equal 6.70479462E-02
: Trying gamma equal 7.45309144E-02
: Gamma decreased to 7.30343238E-02
:
:
: fvalues 0.00000000 25.7253666 25.6717949 25.7253666
:
:
: CGMAT cycle number = 25
:
: function value 25.6717949
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.30343238E-02
: Gamma decreased to 7.16737881E-02
:
:
: fvalues 0.00000000 25.6717949 25.6193657 25.6717949
:
:
: CGMAT cycle number = 26
:
: function value 25.6193657
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.16737881E-02
: Gamma decreased to 7.04369321E-02
:
:
: fvalues 0.00000000 25.6193657 25.5681000 25.6193657
:
:
: CGMAT cycle number = 27
:
: function value 25.5681000
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.04369321E-02
: Gamma decreased to 6.93125203E-02
:
:
: fvalues 0.00000000 25.5681000 25.5180817 25.5681000
:
:
: CGMAT cycle number = 28
:
: function value 25.5180817
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.93125203E-02
: Gamma decreased to 6.82903305E-02
:
:
: fvalues 0.00000000 25.5180817 25.4693146 25.5180817
:
:
: CGMAT cycle number = 29
:
: function value 25.4693146
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.82903305E-02
: Gamma decreased to 6.73610643E-02
:
:
: fvalues 0.00000000 25.4693146 25.4218388 25.4693146
:
:
: CGMAT cycle number = 30
:
: function value 25.4218388
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.73610643E-02
: Gamma decreased to 6.65162802E-02
:
:
: fvalues 0.00000000 25.4218388 25.3756142 25.4218388
:
:
: CGMAT cycle number = 31
:
: function value 25.3756142
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.65162802E-02
: Gamma decreased to 6.57482892E-02
:
:
: fvalues 0.00000000 25.3756142 25.3306885 25.3756142
:
:
: CGMAT cycle number = 32
:
: function value 25.3306885
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.57482892E-02
: Gamma decreased to 6.50501177E-02
:
:
: fvalues 0.00000000 25.3306885 25.2870388 25.3306885
:
:
: CGMAT cycle number = 33
:
: function value 25.2870388
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.50501177E-02
: Gamma decreased to 6.44154176E-02
:
:
: fvalues 0.00000000 25.2870388 25.2447052 25.2870388
:
:
: CGMAT cycle number = 34
:
: function value 25.2447052
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.44154176E-02
: Gamma decreased to 6.38384148E-02
:
:
: fvalues 0.00000000 25.2447052 25.2035961 25.2447052
:
:
: CGMAT cycle number = 35
:
: function value 25.2035961
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.38384148E-02
: Not converging with gamma equal 6.38384148E-02
: Trying gamma equal 6.65922835E-02
: Gamma decreased to 6.60415068E-02
:
:
: fvalues 0.00000000 25.2035961 25.1652355 25.2035961
:
:
: CGMAT cycle number = 36
:
: function value 25.1652355
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.60415068E-02
: Gamma decreased to 6.55408055E-02
:
:
: fvalues 0.00000000 25.1652355 25.1280174 25.1652355
:
:
: CGMAT cycle number = 37
:
: function value 25.1280174
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.55408055E-02
: Gamma decreased to 6.50856197E-02
:
:
: fvalues 0.00000000 25.1280174 25.0918961 25.1280174
:
:
: CGMAT cycle number = 38
:
: function value 25.0918961
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.50856197E-02
: Gamma decreased to 6.46718144E-02
:
:
: fvalues 0.00000000 25.0918961 25.0568581 25.0918961
:
:
: CGMAT cycle number = 39
:
: function value 25.0568581
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.46718144E-02
: Gamma decreased to 6.42956272E-02
:
:
: fvalues 0.00000000 25.0568581 25.0228405 25.0568581
:
:
: CGMAT cycle number = 40
:
: function value 25.0228405
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:Bond angles : refined atoms 40 2.820 3.000
:Bond angles : others 26 0.626 3.000
:Chiral centres: refined atoms 4 0.032 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.067 0.200
:VDW; torsion: refined_atoms 5 0.276 0.200
:VDW; torsion.others 6 0.073 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 6.42956272E-02
: Gamma decreased to 6.39536381E-02
:
:
: fvalues 0.00000000 25.0228405 24.9898758 25.0228405
:
:
: CGMAT cycle number = 1
:
: function value 24.9898758
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:Bond angles : refined atoms 40 2.818 3.000
:Bond angles : others 26 0.626 3.000
:Chiral centres: refined atoms 4 0.032 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.067 0.200
:VDW; torsion: refined_atoms 5 0.276 0.200
:VDW; torsion.others 6 0.074 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.00000000
: Not converging with gamma equal 0.00000000
: Trying gamma equal 5.24999984E-02
: Not converging with gamma equal 5.24999984E-02
: Trying gamma equal 0.107624993
: Gamma decreased to 9.65999961E-02
:
:
: fvalues 0.00000000 24.9898758 24.9701385 24.9898758
:
:
: CGMAT cycle number = 2
:
: function value 24.9701385
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 9.65999961E-02
: Gamma decreased to 8.65772665E-02
:
:
: fvalues 0.00000000 24.9701385 24.9488544 24.9701385
:
:
: CGMAT cycle number = 3
:
: function value 24.9488544
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.65772665E-02
: Gamma decreased to 7.74656981E-02
:
:
: fvalues 0.00000000 24.9488544 24.9259071 24.9488544
:
:
: CGMAT cycle number = 4
:
: function value 24.9259071
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.74656981E-02
: Gamma decreased to 6.91824555E-02
:
:
: fvalues 0.00000000 24.9259071 24.9010849 24.9259071
:
:
: CGMAT cycle number = 5
:
: function value 24.9010849
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.91824555E-02
: Gamma decreased to 6.16522320E-02
:
:
: fvalues 0.00000000 24.9010849 24.8743305 24.9010849
:
:
: CGMAT cycle number = 6
:
: function value 24.8743305
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.16522320E-02
: Gamma decreased to 5.48065752E-02
:
:
: fvalues 0.00000000 24.8743305 24.8454552 24.8743305
:
:
: CGMAT cycle number = 7
:
: function value 24.8454552
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.48065752E-02
: Not converging with gamma equal 5.48065752E-02
: Trying gamma equal 8.74790251E-02
: Gamma decreased to 8.09445381E-02
:
:
: fvalues 0.00000000 24.8454552 24.8252468 24.8454552
:
:
: CGMAT cycle number = 8
:
: function value 24.8252468
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.09445381E-02
: Gamma decreased to 7.50040933E-02
:
:
: fvalues 0.00000000 24.8252468 24.8040237 24.8252468
:
:
: CGMAT cycle number = 9
:
: function value 24.8040237
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.50040933E-02
: Gamma decreased to 6.96036890E-02
:
:
: fvalues 0.00000000 24.8040237 24.7818832 24.8040237
:
:
: CGMAT cycle number = 10
:
: function value 24.7818832
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.96036890E-02
: Gamma decreased to 6.46942332E-02
:
:
: fvalues 0.00000000 24.7818832 24.7587605 24.7818832
:
:
: CGMAT cycle number = 11
:
: function value 24.7587605
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.46942332E-02
: Gamma decreased to 6.02310896E-02
:
:
: fvalues 0.00000000 24.7587605 24.7347507 24.7587605
:
:
: CGMAT cycle number = 12
:
: function value 24.7347507
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.02310896E-02
: Gamma decreased to 5.61736859E-02
:
:
: fvalues 0.00000000 24.7347507 24.7098427 24.7347507
:
:
: CGMAT cycle number = 13
:
: function value 24.7098427
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.61736859E-02
: Not converging with gamma equal 5.61736859E-02
: Trying gamma equal 7.55385682E-02
: Gamma decreased to 7.16655925E-02
:
:
: fvalues 0.00000000 24.7098427 24.6902905 24.7098427
:
:
: CGMAT cycle number = 14
:
: function value 24.6902905
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.16655925E-02
: Gamma decreased to 6.81447089E-02
:
:
: fvalues 0.00000000 24.6902905 24.6702480 24.6902905
:
:
: CGMAT cycle number = 15
:
: function value 24.6702480
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.81447089E-02
: Gamma decreased to 6.49439022E-02
:
:
: fvalues 0.00000000 24.6702480 24.6498699 24.6702480
:
:
: CGMAT cycle number = 16
:
: function value 24.6498699
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.49439022E-02
: Gamma decreased to 6.20340779E-02
:
:
: fvalues 0.00000000 24.6498699 24.6290627 24.6498699
:
:
: CGMAT cycle number = 17
:
: function value 24.6290627
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.20340779E-02
: Gamma decreased to 5.93887828E-02
:
:
: fvalues 0.00000000 24.6290627 24.6079788 24.6290627
:
:
: CGMAT cycle number = 18
:
: function value 24.6079788
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.93887828E-02
: Gamma decreased to 5.69839701E-02
:
:
: fvalues 0.00000000 24.6079788 24.5866604 24.6079788
:
:
: CGMAT cycle number = 19
:
: function value 24.5866604
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.69839701E-02
: Not converging with gamma equal 5.69839701E-02
: Trying gamma equal 6.84614852E-02
: Gamma decreased to 6.61659837E-02
:
:
: fvalues 0.00000000 24.5866604 24.5685177 24.5866604
:
:
: CGMAT cycle number = 20
:
: function value 24.5685177
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.61659837E-02
: Gamma decreased to 6.40791655E-02
:
:
: fvalues 0.00000000 24.5685177 24.5502567 24.5685177
:
:
: CGMAT cycle number = 21
:
: function value 24.5502567
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.40791655E-02
: Gamma decreased to 6.21820539E-02
:
:
: fvalues 0.00000000 24.5502567 24.5319290 24.5502567
:
:
: CGMAT cycle number = 22
:
: function value 24.5319290
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.21820539E-02
: Gamma decreased to 6.04574084E-02
:
:
: fvalues 0.00000000 24.5319290 24.5135536 24.5319290
:
:
: CGMAT cycle number = 23
:
: function value 24.5135536
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.04574084E-02
: Gamma decreased to 5.88895492E-02
:
:
: fvalues 0.00000000 24.5135536 24.4952602 24.5135536
:
:
: CGMAT cycle number = 24
:
: function value 24.4952602
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.88895492E-02
: Gamma decreased to 5.74642234E-02
:
:
: fvalues 0.00000000 24.4952602 24.4769573 24.4952602
:
:
: CGMAT cycle number = 25
:
: function value 24.4769573
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.74642234E-02
: Gamma decreased to 5.61684705E-02
:
:
: fvalues 0.00000000 24.4769573 24.4587746 24.4769573
:
:
: CGMAT cycle number = 26
:
: function value 24.4587746
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.61684705E-02
: Gamma decreased to 5.49905151E-02
:
:
: fvalues 0.00000000 24.4587746 24.4407291 24.4587746
:
:
: CGMAT cycle number = 27
:
: function value 24.4407291
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.49905151E-02
: Not converging with gamma equal 5.49905151E-02
: Trying gamma equal 6.06125779E-02
: Gamma decreased to 5.94881661E-02
:
:
: fvalues 0.00000000 24.4407291 24.4243298 24.4407291
:
:
: CGMAT cycle number = 28
:
: function value 24.4243298
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.94881661E-02
: Gamma decreased to 5.84659725E-02
:
:
: fvalues 0.00000000 24.4243298 24.4081230 24.4243298
:
:
: CGMAT cycle number = 29
:
: function value 24.4081230
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.84659725E-02
: Gamma decreased to 5.75367063E-02
:
:
: fvalues 0.00000000 24.4081230 24.3920441 24.4081230
:
:
: CGMAT cycle number = 30
:
: function value 24.3920441
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.75367063E-02
: Gamma decreased to 5.66919185E-02
:
:
: fvalues 0.00000000 24.3920441 24.3761597 24.3920441
:
:
: CGMAT cycle number = 31
:
: function value 24.3761597
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.66919185E-02
: Gamma decreased to 5.59239313E-02
:
:
: fvalues 0.00000000 24.3761597 24.3604450 24.3761597
:
:
: CGMAT cycle number = 32
:
: function value 24.3604450
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.59239313E-02
: Gamma decreased to 5.52257597E-02
:
:
: fvalues 0.00000000 24.3604450 24.3450127 24.3604450
:
:
: CGMAT cycle number = 33
:
: function value 24.3450127
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.52257597E-02
: Not converging with gamma equal 5.52257597E-02
: Trying gamma equal 5.85579425E-02
: Gamma decreased to 5.78915067E-02
:
:
: fvalues 0.00000000 24.3450127 24.3305473 24.3450127
:
:
: CGMAT cycle number = 34
:
: function value 24.3305473
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.78915067E-02
: Gamma decreased to 5.72856553E-02
:
:
: fvalues 0.00000000 24.3305473 24.3163261 24.3305473
:
:
: CGMAT cycle number = 35
:
: function value 24.3163261
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.72856553E-02
: Gamma decreased to 5.67348823E-02
:
:
: fvalues 0.00000000 24.3163261 24.3023262 24.3163261
:
:
: CGMAT cycle number = 36
:
: function value 24.3023262
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.67348823E-02
: Gamma decreased to 5.62341772E-02
:
:
: fvalues 0.00000000 24.3023262 24.2885036 24.3023262
:
:
: CGMAT cycle number = 37
:
: function value 24.2885036
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.62341772E-02
: Gamma decreased to 5.57789914E-02
:
:
: fvalues 0.00000000 24.2885036 24.2749252 24.2885036
:
:
: CGMAT cycle number = 38
:
: function value 24.2749252
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.57789914E-02
: Gamma decreased to 5.53651862E-02
:
:
: fvalues 0.00000000 24.2749252 24.2615910 24.2749252
:
:
: CGMAT cycle number = 39
:
: function value 24.2615910
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.53651862E-02
: Gamma decreased to 5.49889989E-02
:
:
: fvalues 0.00000000 24.2615910 24.2484512 24.2615910
:
:
: CGMAT cycle number = 40
:
: function value 24.2484512
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:Bond angles : refined atoms 40 2.752 3.000
:Bond angles : others 26 0.628 3.000
:Chiral centres: refined atoms 4 0.031 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 1 0.096 0.200
:VDW; torsion: refined_atoms 5 0.277 0.200
:VDW; torsion.others 6 0.079 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 5.49889989E-02
: Gamma decreased to 5.46470098E-02
:
:
: fvalues 0.00000000 24.2484512 24.2356129 24.2484512
:
:
: CGMAT cycle number = 1
:
: function value 24.2356129
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:Bond angles : refined atoms 40 2.751 3.000
:Bond angles : others 26 0.628 3.000
:Chiral centres: refined atoms 4 0.031 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 1 0.096 0.200
:VDW; torsion: refined_atoms 5 0.277 0.200
:VDW; torsion.others 6 0.079 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.00000000
: Not converging with gamma equal 0.00000000
: Trying gamma equal 5.24999984E-02
: Gamma decreased to 4.19999994E-02
:
:
: fvalues 0.00000000 24.2356129 24.2226276 24.2356129
:
:
: CGMAT cycle number = 2
:
: function value 24.2226276
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19999994E-02
: Not converging with gamma equal 4.19999994E-02
: Trying gamma equal 9.21136290E-02
: Gamma decreased to 8.20908993E-02
:
:
: fvalues 0.00000000 24.2226276 24.2150688 24.2226276
:
:
: CGMAT cycle number = 3
:
: function value 24.2150688
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.20908993E-02
: Gamma decreased to 7.29793310E-02
:
:
: fvalues 0.00000000 24.2150688 24.2067719 24.2150688
:
:
: CGMAT cycle number = 4
:
: function value 24.2067719
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.29793310E-02
: Gamma decreased to 6.46960884E-02
:
:
: fvalues 0.00000000 24.2067719 24.1977005 24.2067719
:
:
: CGMAT cycle number = 5
:
: function value 24.1977005
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.46960884E-02
: Gamma decreased to 5.71658649E-02
:
:
: fvalues 0.00000000 24.1977005 24.1877708 24.1977005
:
:
: CGMAT cycle number = 6
:
: function value 24.1877708
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.71658649E-02
: Gamma decreased to 5.03202081E-02
:
:
: fvalues 0.00000000 24.1877708 24.1768131 24.1877708
:
:
: CGMAT cycle number = 7
:
: function value 24.1768131
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.03202081E-02
: Gamma decreased to 4.40968834E-02
:
:
: fvalues 0.00000000 24.1768131 24.1646919 24.1768131
:
:
: CGMAT cycle number = 8
:
: function value 24.1646919
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.40968834E-02
: Not converging with gamma equal 4.40968834E-02
: Trying gamma equal 7.37991035E-02
: Gamma decreased to 6.78586587E-02
:
:
: fvalues 0.00000000 24.1646919 24.1564713 24.1646919
:
:
: CGMAT cycle number = 9
:
: function value 24.1564713
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.78586587E-02
: Gamma decreased to 6.24582544E-02
:
:
: fvalues 0.00000000 24.1564713 24.1476917 24.1564713
:
:
: CGMAT cycle number = 10
:
: function value 24.1476917
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.24582544E-02
: Gamma decreased to 5.75487949E-02
:
:
: fvalues 0.00000000 24.1476917 24.1383801 24.1476917
:
:
: CGMAT cycle number = 11
:
: function value 24.1383801
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.75487949E-02
: Gamma decreased to 5.30856512E-02
:
:
: fvalues 0.00000000 24.1383801 24.1285248 24.1383801
:
:
: CGMAT cycle number = 12
:
: function value 24.1285248
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.30856512E-02
: Gamma decreased to 4.90282476E-02
:
:
: fvalues 0.00000000 24.1285248 24.1180897 24.1285248
:
:
: CGMAT cycle number = 13
:
: function value 24.1180897
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.90282476E-02
: Not converging with gamma equal 4.90282476E-02
: Trying gamma equal 6.83931261E-02
: Gamma decreased to 6.45201504E-02
:
:
: fvalues 0.00000000 24.1180897 24.1100349 24.1180897
:
:
: CGMAT cycle number = 14
:
: function value 24.1100349
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.45201504E-02
: Gamma decreased to 6.09992631E-02
:
:
: fvalues 0.00000000 24.1100349 24.1017036 24.1100349
:
:
: CGMAT cycle number = 15
:
: function value 24.1017036
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.09992631E-02
: Gamma decreased to 5.77984564E-02
:
:
: fvalues 0.00000000 24.1017036 24.0930786 24.1017036
:
:
: CGMAT cycle number = 16
:
: function value 24.0930786
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.77984564E-02
: Gamma decreased to 5.48886321E-02
:
:
: fvalues 0.00000000 24.0930786 24.0841446 24.0930786
:
:
: CGMAT cycle number = 17
:
: function value 24.0841446
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.48886321E-02
: Gamma decreased to 5.22433370E-02
:
:
: fvalues 0.00000000 24.0841446 24.0750084 24.0841446
:
:
: CGMAT cycle number = 18
:
: function value 24.0750084
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.22433370E-02
: Gamma decreased to 4.98385243E-02
:
:
: fvalues 0.00000000 24.0750084 24.0655861 24.0750084
:
:
: CGMAT cycle number = 19
:
: function value 24.0655861
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.98385243E-02
: Not converging with gamma equal 4.98385243E-02
: Trying gamma equal 6.13160431E-02
: Gamma decreased to 5.90205416E-02
:
:
: fvalues 0.00000000 24.0655861 24.0576439 24.0655861
:
:
: CGMAT cycle number = 20
:
: function value 24.0576439
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.90205416E-02
: Gamma decreased to 5.69337197E-02
:
:
: fvalues 0.00000000 24.0576439 24.0495739 24.0576439
:
:
: CGMAT cycle number = 21
:
: function value 24.0495739
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.69337197E-02
: Gamma decreased to 5.50366081E-02
:
:
: fvalues 0.00000000 24.0495739 24.0414257 24.0495739
:
:
: CGMAT cycle number = 22
:
: function value 24.0414257
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.50366081E-02
: Gamma decreased to 5.33119626E-02
:
:
: fvalues 0.00000000 24.0414257 24.0331345 24.0414257
:
:
: CGMAT cycle number = 23
:
: function value 24.0331345
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.33119626E-02
: Gamma decreased to 5.17441034E-02
:
:
: fvalues 0.00000000 24.0331345 24.0247498 24.0331345
:
:
: CGMAT cycle number = 24
:
: function value 24.0247498
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.17441034E-02
: Not converging with gamma equal 5.17441034E-02
: Trying gamma equal 5.92270717E-02
: Gamma decreased to 5.77304773E-02
:
:
: fvalues 0.00000000 24.0247498 24.0173187 24.0247498
:
:
: CGMAT cycle number = 25
:
: function value 24.0173187
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.77304773E-02
: Gamma decreased to 5.63699380E-02
:
:
: fvalues 0.00000000 24.0173187 24.0098381 24.0173187
:
:
: CGMAT cycle number = 26
:
: function value 24.0098381
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.007 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.63699380E-02
: Gamma decreased to 5.51330857E-02
:
:
: fvalues 0.00000000 24.0098381 24.0023270 24.0098381
:
:
: CGMAT cycle number = 27
:
: function value 24.0023270
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.51330857E-02
: Gamma decreased to 5.40086739E-02
:
:
: fvalues 0.00000000 24.0023270 23.9948082 24.0023270
:
:
: CGMAT cycle number = 28
:
: function value 23.9948082
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.40086739E-02
: Gamma decreased to 5.29864803E-02
:
:
: fvalues 0.00000000 23.9948082 23.9873085 23.9948082
:
:
: CGMAT cycle number = 29
:
: function value 23.9873085
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.29864803E-02
: Gamma decreased to 5.20572141E-02
:
:
: fvalues 0.00000000 23.9873085 23.9797935 23.9873085
:
:
: CGMAT cycle number = 30
:
: function value 23.9797935
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.20572141E-02
: Not converging with gamma equal 5.20572141E-02
: Trying gamma equal 5.64923510E-02
: Gamma decreased to 5.56053221E-02
:
:
: fvalues 0.00000000 23.9797935 23.9728737 23.9797935
:
:
: CGMAT cycle number = 31
:
: function value 23.9728737
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.56053221E-02
: Gamma decreased to 5.47989346E-02
:
:
: fvalues 0.00000000 23.9728737 23.9659901 23.9728737
:
:
: CGMAT cycle number = 32
:
: function value 23.9659901
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.47989346E-02
: Gamma decreased to 5.40658534E-02
:
:
: fvalues 0.00000000 23.9659901 23.9591103 23.9659901
:
:
: CGMAT cycle number = 33
:
: function value 23.9591103
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.40658534E-02
: Gamma decreased to 5.33994175E-02
:
:
: fvalues 0.00000000 23.9591103 23.9523029 23.9591103
:
:
: CGMAT cycle number = 34
:
: function value 23.9523029
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.33994175E-02
: Gamma decreased to 5.27935661E-02
:
:
: fvalues 0.00000000 23.9523029 23.9455223 23.9523029
:
:
: CGMAT cycle number = 35
:
: function value 23.9455223
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.27935661E-02
: Gamma decreased to 5.22427931E-02
:
:
: fvalues 0.00000000 23.9455223 23.9388161 23.9455223
:
:
: CGMAT cycle number = 36
:
: function value 23.9388161
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.22427931E-02
: Not converging with gamma equal 5.22427931E-02
: Trying gamma equal 5.48714884E-02
: Gamma decreased to 5.43457493E-02
:
:
: fvalues 0.00000000 23.9388161 23.9324512 23.9388161
:
:
: CGMAT cycle number = 37
:
: function value 23.9324512
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.43457493E-02
: Gamma decreased to 5.38678057E-02
:
:
: fvalues 0.00000000 23.9324512 23.9261417 23.9324512
:
:
: CGMAT cycle number = 38
:
: function value 23.9261417
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.38678057E-02
: Not converging with gamma equal 5.38678057E-02
: Trying gamma equal 5.61489053E-02
: Gamma decreased to 5.56926839E-02
:
:
: fvalues 0.00000000 23.9261417 23.9201393 23.9261417
:
:
: CGMAT cycle number = 39
:
: function value 23.9201393
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.56926839E-02
: Gamma decreased to 5.52779399E-02
:
:
: fvalues 0.00000000 23.9201393 23.9141579 23.9201393
:
:
: CGMAT cycle number = 40
:
: function value 23.9141579
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:Bond angles : refined atoms 40 2.720 3.000
:Bond angles : others 26 0.628 3.000
:Chiral centres: refined atoms 4 0.030 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.069 0.200
:VDW; torsion: refined_atoms 5 0.278 0.200
:VDW; torsion.others 6 0.082 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 5.52779399E-02
: Gamma decreased to 5.49008995E-02
:
:
: fvalues 0.00000000 23.9141579 23.9082661 23.9141579
:
: **** Final optimisation stage ****
:
:
:
: CGMAT cycle number = 1
:
: function value 23.9082661
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:Bond angles : refined atoms 40 2.720 3.000
:Bond angles : others 26 0.628 3.000
:Chiral centres: refined atoms 4 0.030 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.069 0.200
:VDW; torsion: refined_atoms 5 0.278 0.200
:VDW; torsion.others 6 0.082 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 0.00000000
: Not converging with gamma equal 0.00000000
: Trying gamma equal 5.24999984E-02
: Gamma decreased to 4.19999994E-02
:
:
: fvalues 0.00000000 23.9082661 23.9022408 23.9082661
:
:
: CGMAT cycle number = 2
:
: function value 23.9022408
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.19999994E-02
: Not converging with gamma equal 4.19999994E-02
: Trying gamma equal 9.21136290E-02
: Gamma decreased to 8.20908993E-02
:
:
: fvalues 0.00000000 23.9022408 23.8987045 23.9022408
:
:
: CGMAT cycle number = 3
:
: function value 23.8987045
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 8.20908993E-02
: Gamma decreased to 7.29793310E-02
:
:
: fvalues 0.00000000 23.8987045 23.8948288 23.8987045
:
:
: CGMAT cycle number = 4
:
: function value 23.8948288
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 7.29793310E-02
: Gamma decreased to 6.46960884E-02
:
:
: fvalues 0.00000000 23.8948288 23.8905411 23.8948288
:
:
: CGMAT cycle number = 5
:
: function value 23.8905411
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.46960884E-02
: Gamma decreased to 5.71658649E-02
:
:
: fvalues 0.00000000 23.8905411 23.8858585 23.8905411
:
:
: CGMAT cycle number = 6
:
: function value 23.8858585
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.71658649E-02
: Gamma decreased to 5.03202081E-02
:
:
: fvalues 0.00000000 23.8858585 23.8806114 23.8858585
:
:
: CGMAT cycle number = 7
:
: function value 23.8806114
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.03202081E-02
: Gamma decreased to 4.40968834E-02
:
:
: fvalues 0.00000000 23.8806114 23.8748360 23.8806114
:
:
: CGMAT cycle number = 8
:
: function value 23.8748360
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.40968834E-02
: Not converging with gamma equal 4.40968834E-02
: Trying gamma equal 7.37991035E-02
: Gamma decreased to 6.78586587E-02
:
:
: fvalues 0.00000000 23.8748360 23.8708134 23.8748360
:
:
: CGMAT cycle number = 9
:
: function value 23.8708134
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.78586587E-02
: Gamma decreased to 6.24582544E-02
:
:
: fvalues 0.00000000 23.8708134 23.8665676 23.8708134
:
:
: CGMAT cycle number = 10
:
: function value 23.8665676
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.24582544E-02
: Gamma decreased to 5.75487949E-02
:
:
: fvalues 0.00000000 23.8665676 23.8619900 23.8665676
:
:
: CGMAT cycle number = 11
:
: function value 23.8619900
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.75487949E-02
: Gamma decreased to 5.30856512E-02
:
:
: fvalues 0.00000000 23.8619900 23.8571739 23.8619900
:
:
: CGMAT cycle number = 12
:
: function value 23.8571739
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.30856512E-02
: Gamma decreased to 4.90282476E-02
:
:
: fvalues 0.00000000 23.8571739 23.8520317 23.8571739
:
:
: CGMAT cycle number = 13
:
: function value 23.8520317
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 4.90282476E-02
: Not converging with gamma equal 4.90282476E-02
: Trying gamma equal 6.83931261E-02
: Gamma decreased to 6.45201504E-02
:
:
: fvalues 0.00000000 23.8520317 23.8480072 23.8520317
:
:
: CGMAT cycle number = 14
:
: function value 23.8480072
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.45201504E-02
: Gamma decreased to 6.09992631E-02
:
:
: fvalues 0.00000000 23.8480072 23.8438416 23.8480072
:
:
: CGMAT cycle number = 15
:
: function value 23.8438416
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.09992631E-02
: Gamma decreased to 5.77984564E-02
:
:
: fvalues 0.00000000 23.8438416 23.8394718 23.8438416
:
:
: CGMAT cycle number = 16
:
: function value 23.8394718
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.77984564E-02
: Gamma decreased to 5.48886321E-02
:
:
: fvalues 0.00000000 23.8394718 23.8350353 23.8394718
:
:
: CGMAT cycle number = 17
:
: function value 23.8350353
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.48886321E-02
: Gamma decreased to 5.22433370E-02
:
:
: fvalues 0.00000000 23.8350353 23.8303623 23.8350353
:
:
: CGMAT cycle number = 18
:
: function value 23.8303623
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.22433370E-02
: Not converging with gamma equal 5.22433370E-02
: Trying gamma equal 6.48686066E-02
: Gamma decreased to 6.23435527E-02
:
:
: fvalues 0.00000000 23.8303623 23.8264084 23.8303623
:
:
: CGMAT cycle number = 19
:
: function value 23.8264084
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.23435527E-02
: Gamma decreased to 6.00480475E-02
:
:
: fvalues 0.00000000 23.8264084 23.8223915 23.8264084
:
:
: CGMAT cycle number = 20
:
: function value 23.8223915
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 6.00480475E-02
: Gamma decreased to 5.79612255E-02
:
:
: fvalues 0.00000000 23.8223915 23.8182735 23.8223915
:
:
: CGMAT cycle number = 21
:
: function value 23.8182735
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.79612255E-02
: Gamma decreased to 5.60641140E-02
:
:
: fvalues 0.00000000 23.8182735 23.8141041 23.8182735
:
:
: CGMAT cycle number = 22
:
: function value 23.8141041
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.60641140E-02
: Gamma decreased to 5.43394685E-02
:
:
: fvalues 0.00000000 23.8141041 23.8098297 23.8141041
:
:
: CGMAT cycle number = 23
:
: function value 23.8098297
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.43394685E-02
: Gamma decreased to 5.27716093E-02
:
:
: fvalues 0.00000000 23.8098297 23.8054962 23.8098297
:
:
: CGMAT cycle number = 24
:
: function value 23.8054962
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.27716093E-02
: Gamma decreased to 5.13462834E-02
:
:
: fvalues 0.00000000 23.8054962 23.8011284 23.8054962
:
:
: CGMAT cycle number = 25
:
: function value 23.8011284
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.13462834E-02
: Not converging with gamma equal 5.13462834E-02
: Trying gamma equal 5.81489801E-02
: Gamma decreased to 5.67884408E-02
:
:
: fvalues 0.00000000 23.8011284 23.7971725 23.8011284
:
:
: CGMAT cycle number = 26
:
: function value 23.7971725
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.67884408E-02
: Gamma decreased to 5.55515885E-02
:
:
: fvalues 0.00000000 23.7971725 23.7931995 23.7971725
:
:
: CGMAT cycle number = 27
:
: function value 23.7931995
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.55515885E-02
: Gamma decreased to 5.44271767E-02
:
:
: fvalues 0.00000000 23.7931995 23.7891808 23.7931995
:
:
: CGMAT cycle number = 28
:
: function value 23.7891808
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.44271767E-02
: Gamma decreased to 5.34049831E-02
:
:
: fvalues 0.00000000 23.7891808 23.7851563 23.7891808
:
:
: CGMAT cycle number = 29
:
: function value 23.7851563
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.34049831E-02
: Not converging with gamma equal 5.34049831E-02
: Trying gamma equal 5.82836345E-02
: Gamma decreased to 5.73079064E-02
:
:
: fvalues 0.00000000 23.7851563 23.7814083 23.7851563
:
:
: CGMAT cycle number = 30
:
: function value 23.7814083
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.73079064E-02
: Gamma decreased to 5.64208776E-02
:
:
: fvalues 0.00000000 23.7814083 23.7777004 23.7814083
:
:
: CGMAT cycle number = 31
:
: function value 23.7777004
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.64208776E-02
: Gamma decreased to 5.56144901E-02
:
:
: fvalues 0.00000000 23.7777004 23.7739315 23.7777004
:
:
: CGMAT cycle number = 32
:
: function value 23.7739315
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.56144901E-02
: Gamma decreased to 5.48814088E-02
:
:
: fvalues 0.00000000 23.7739315 23.7702103 23.7739315
:
:
: CGMAT cycle number = 33
:
: function value 23.7702103
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.48814088E-02
: Gamma decreased to 5.42149730E-02
:
:
: fvalues 0.00000000 23.7702103 23.7664757 23.7702103
:
:
: CGMAT cycle number = 34
:
: function value 23.7664757
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.42149730E-02
: Gamma decreased to 5.36091216E-02
:
:
: fvalues 0.00000000 23.7664757 23.7627697 23.7664757
:
:
: CGMAT cycle number = 35
:
: function value 23.7627697
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.36091216E-02
: Gamma decreased to 5.30583486E-02
:
:
: fvalues 0.00000000 23.7627697 23.7590618 23.7627697
:
:
: CGMAT cycle number = 36
:
: function value 23.7590618
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.30583486E-02
: Not converging with gamma equal 5.30583486E-02
: Trying gamma equal 5.56870438E-02
: Gamma decreased to 5.51613048E-02
:
:
: fvalues 0.00000000 23.7590618 23.7555161 23.7590618
:
:
: CGMAT cycle number = 37
:
: function value 23.7555161
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.51613048E-02
: Gamma decreased to 5.46833612E-02
:
:
: fvalues 0.00000000 23.7555161 23.7519722 23.7555161
:
:
: CGMAT cycle number = 38
:
: function value 23.7519722
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.46833612E-02
: Gamma decreased to 5.42488657E-02
:
:
: fvalues 0.00000000 23.7519722 23.7485046 23.7519722
:
:
: CGMAT cycle number = 39
:
: function value 23.7485046
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:-------------------------------------------------------------------------------
: Trying gamma equal 5.42488657E-02
: Not converging with gamma equal 5.42488657E-02
: Trying gamma equal 5.63225895E-02
: Gamma decreased to 5.59078455E-02
:
:
: fvalues 0.00000000 23.7485046 23.7451267 23.7485046
:
:
: CGMAT cycle number = 40
:
: function value 23.7451267
:
:-------------------------------------------------------------------------------
: Restraint type N restraints Rms Delta Av(Sigma)
:Bond distances: refined atoms 26 0.006 0.020
:Bond distances: others 12 0.000 0.020
:Bond angles : refined atoms 40 2.703 3.000
:Bond angles : others 26 0.628 3.000
:Chiral centres: refined atoms 4 0.030 0.200
:Planar groups: refined atoms 14 0.000 0.020
:Planar groups: others 6 0.000 0.020
:VDW repulsions.others 2 0.069 0.200
:VDW; torsion: refined_atoms 5 0.278 0.200
:VDW; torsion.others 6 0.084 0.200
:-------------------------------------------------------------------------------
: Trying gamma equal 5.59078455E-02
: Gamma decreased to 5.55308051E-02
:
:
: fvalues 0.00000000 23.7451267 23.7417908 23.7451267
: chir_max = 4.76863384E-02
: rms = 0.324819803
: angle = 0.906694055
: Time in seconds: CPU = 0.49
: 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 0.0093 0.463 3.119 1.040 0.035
: 2 0.0 0.0 0.0 0. 0.0 0.0068 0.339 3.038 1.013 0.031
: 3 0.0 0.0 0.0 0. 0.0 0.0067 0.334 3.019 1.006 0.031
: 4 0.0 0.0 0.0 0. 0.0 0.0066 0.332 3.008 1.003 0.031
: 5 0.0 0.0 0.0 0. 0.0 0.0066 0.332 2.998 0.999 0.032
: 6 0.0 0.0 0.0 0. 0.0 0.0066 0.332 2.988 0.996 0.033
: 7 0.0 0.0 0.0 0. 0.0 0.0066 0.332 2.979 0.993 0.033
: 8 0.0 0.0 0.0 0. 0.0 0.0066 0.332 2.970 0.990 0.034
: 9 0.0 0.0 0.0 0. 0.0 0.0066 0.332 2.961 0.987 0.034
: 10 0.0 0.0 0.0 0. 0.0 0.0066 0.331 2.953 0.984 0.034
: 11 0.0 0.0 0.0 0. 0.0 0.0066 0.331 2.946 0.982 0.034
: 12 0.0 0.0 0.0 0. 0.0 0.0066 0.331 2.939 0.980 0.035
: 13 0.0 0.0 0.0 0. 0.0 0.0066 0.331 2.933 0.978 0.035
: 14 0.0 0.0 0.0 0. 0.0 0.0066 0.331 2.926 0.975 0.034
: 15 0.0 0.0 0.0 0. 0.0 0.0066 0.331 2.920 0.973 0.034
: 16 0.0 0.0 0.0 0. 0.0 0.0066 0.330 2.914 0.971 0.034
: 17 0.0 0.0 0.0 0. 0.0 0.0066 0.330 2.909 0.970 0.034
: 18 0.0 0.0 0.0 0. 0.0 0.0066 0.330 2.904 0.968 0.034
: 19 0.0 0.0 0.0 0. 0.0 0.0066 0.330 2.898 0.966 0.034
: 20 0.0 0.0 0.0 0. 0.0 0.0066 0.330 2.893 0.964 0.034
: 21 0.0 0.0 0.0 0. 0.0 0.0066 0.330 2.888 0.963 0.034
: 22 0.0 0.0 0.0 0. 0.0 0.0066 0.330 2.883 0.961 0.034
: 23 0.0 0.0 0.0 0. 0.0 0.0066 0.329 2.879 0.960 0.034
: 24 0.0 0.0 0.0 0. 0.0 0.0066 0.329 2.874 0.958 0.034
: 25 0.0 0.0 0.0 0. 0.0 0.0066 0.329 2.870 0.957 0.033
: 26 0.0 0.0 0.0 0. 0.0 0.0066 0.329 2.866 0.955 0.033
: 27 0.0 0.0 0.0 0. 0.0 0.0066 0.329 2.862 0.954 0.033
: 28 0.0 0.0 0.0 0. 0.0 0.0066 0.329 2.858 0.953 0.033
: 29 0.0 0.0 0.0 0. 0.0 0.0066 0.329 2.854 0.951 0.033
: 30 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.850 0.950 0.033
: 31 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.846 0.949 0.033
: 32 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.843 0.948 0.033
: 33 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.839 0.946 0.033
: 34 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.836 0.945 0.033
: 35 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.833 0.944 0.033
: 36 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.829 0.943 0.033
: 37 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.826 0.942 0.032
: 38 0.0 0.0 0.0 0. 0.0 0.0066 0.328 2.823 0.941 0.032
: 39 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.820 0.940 0.032
: 40 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.818 0.939 0.032
: 41 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.816 0.939 0.032
: 42 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.814 0.938 0.032
: 43 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.812 0.937 0.032
: 44 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.810 0.937 0.032
: 45 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.808 0.936 0.032
: 46 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.805 0.935 0.032
: 47 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.803 0.934 0.032
: 48 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.802 0.934 0.032
: 49 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.800 0.933 0.032
: 50 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.798 0.933 0.032
: 51 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.796 0.932 0.032
: 52 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.793 0.931 0.032
: 53 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.792 0.931 0.032
: 54 0.0 0.0 0.0 0. 0.0 0.0065 0.327 2.790 0.930 0.032
: 55 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.788 0.929 0.032
: 56 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.786 0.929 0.032
: 57 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.784 0.928 0.032
: 58 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.782 0.927 0.032
: 59 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.781 0.927 0.031
: 60 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.779 0.926 0.031
: 61 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.778 0.926 0.031
: 62 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.776 0.925 0.031
: 63 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.774 0.925 0.031
: 64 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.773 0.924 0.031
: 65 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.771 0.924 0.031
: 66 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.769 0.923 0.031
: 67 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.768 0.923 0.031
: 68 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.766 0.922 0.031
: 69 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.765 0.922 0.031
: 70 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.763 0.921 0.031
: 71 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.762 0.921 0.031
: 72 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.761 0.920 0.031
: 73 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.759 0.920 0.031
: 74 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.758 0.919 0.031
: 75 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.757 0.919 0.031
: 76 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.755 0.918 0.031
: 77 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.754 0.918 0.031
: 78 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.753 0.918 0.031
: 79 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.752 0.917 0.031
: 80 0.0 0.0 0.0 0. 0.0 0.0065 0.326 2.751 0.917 0.031
: 81 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.749 0.916 0.031
: 82 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.749 0.916 0.031
: 83 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.748 0.916 0.031
: 84 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.747 0.916 0.031
: 85 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.746 0.915 0.031
: 86 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.745 0.915 0.031
: 87 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.744 0.915 0.031
: 88 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.743 0.914 0.031
: 89 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.742 0.914 0.031
: 90 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.741 0.914 0.031
: 91 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.741 0.914 0.031
: 92 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.740 0.913 0.031
: 93 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.739 0.913 0.031
: 94 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.738 0.913 0.031
: 95 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.737 0.912 0.031
: 96 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.736 0.912 0.031
: 97 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.736 0.912 0.030
: 98 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.735 0.912 0.030
: 99 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.734 0.911 0.030
: 100 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.733 0.911 0.030
: 101 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.732 0.911 0.030
: 102 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.732 0.911 0.030
: 103 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.731 0.910 0.030
: 104 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.730 0.910 0.030
: 105 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.729 0.910 0.030
: 106 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.729 0.910 0.030
: 107 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.728 0.909 0.030
: 108 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.727 0.909 0.030
: 109 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.726 0.909 0.030
: 110 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.726 0.909 0.030
: 111 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.725 0.908 0.030
: 112 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.724 0.908 0.030
: 113 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.724 0.908 0.030
: 114 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.723 0.908 0.030
: 115 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.722 0.907 0.030
: 116 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.722 0.907 0.030
: 117 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.721 0.907 0.030
: 118 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.721 0.907 0.030
: 119 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.720 0.907 0.030
: 120 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.720 0.907 0.030
: 121 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.719 0.906 0.030
: 122 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.719 0.906 0.030
: 123 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.718 0.906 0.030
: 124 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.718 0.906 0.030
: 125 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.717 0.906 0.030
: 126 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.717 0.906 0.030
: 127 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.716 0.905 0.030
: 128 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.716 0.905 0.030
: 129 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.715 0.905 0.030
: 130 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.715 0.905 0.030
: 131 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.715 0.905 0.030
: 132 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.714 0.905 0.030
: 133 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.714 0.905 0.030
: 134 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.713 0.904 0.030
: 135 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.713 0.904 0.030
: 136 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.712 0.904 0.030
: 137 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.712 0.904 0.030
: 138 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.712 0.904 0.030
: 139 0.0 0.0 0.0 0. 0.0 0INFO:: 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
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 109 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Mon_May_14_11:46:54_2018_modification_0.pdb.gz
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Mon_May_14_11:46:54_2018_modification_1.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-3GP.pdb
PDB file /home/paule/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 110 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Mon_May_14_11:46:54_2018_modification_0.pdb.gz
INFO:: comp-id: LIG is marked for non-autoloading - stopping now
INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb
PDB file /home/paule/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 111 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: comp-id: LIG is marked for non-autoloading - stopping now
INFO:: comp-id: LIG is marked for non-autoloading - stopping now
INFO:: Reading coordinate file: /home/paule/data/greg-data/test-LIG.pdb
PDB file /home/paule/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 112 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: comp-id: LIG is marked for non-autoloading - stopping now
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Mon_May_14_11:46:54_2018_modification_2.pdb.gz
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring
INFO:: Reading coordinate file: /home/paule/data/greg-data/monomer-NPO.pdb
PDB file /home/paule/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 113 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
PDB file /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 119 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.144 seconds to read MTZ file
INFO:: 0.092 seconds to initialize map
INFO:: 0.085 seconds for FFT
INFO:: 0.012 seconds for statistics
Map mean: ........ -8.79e-07
Map sigma: ....... 0.1712
Map maximum: ..... 1.343
Map minimum: ..... -0.6954
INFO:: 0.006 seconds for contour map
INFO:: 0.339 seconds in total
INFO:: making difference map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.088 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.078 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:: 0.181 seconds in total
INFO:: ligand number 0 is molecule number 113 with wiggly flag: 0
in execute_ligand_search_internal() import maps from mol 120
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 102889
-0.02498 142998
0.01126 471776
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
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -370.2
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 11) at -469.6
Final Estimated RMS Z Scores:
bonds: 0.3645
angles: 0.1297
torsions: N/A
planes: 0.1993
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 33.47
Removing idle function -1
Refinement elapsed time: 0.023
INFO:: backup file coot-backup/Fitted_ligand_#0-0_Mon_May_14_11:46:59_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.018 and 8 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -137.5
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 2) at -253.7
Final Estimated RMS Z Scores:
bonds: 0.1551
angles: 0.1659
torsions: N/A
planes: 0.1582
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 34.44
Removing idle function -1
Refinement elapsed time: 0.091
INFO:: backup file coot-backup/Fitted_ligand_#1-0_Mon_May_14_11:47:00_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.09 and 4 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -152
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 26) at -242.5
Final Estimated RMS Z Scores:
bonds: 0.2189
angles: 0.09232
torsions: N/A
planes: 0.06772
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 34.92
Removing idle function -1
Refinement elapsed time: 0.035
INFO:: backup file coot-backup/Fitted_ligand_#2-0_Mon_May_14_11:47:00_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.859 and 6 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -78.04
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 72) at -174.1
Final Estimated RMS Z Scores:
bonds: 0.1941
angles: 0.1074
torsions: N/A
planes: 0.1741
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 35.59
Removing idle function -1
Refinement elapsed time: 0.025
INFO:: backup file coot-backup/Fitted_ligand_#3-0_Mon_May_14_11:47:01_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.391 and 10 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -18.54
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 43) at -205.3
Final Estimated RMS Z Scores:
bonds: 0.2753
angles: 0.1072
torsions: N/A
planes: 0.3154
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 36.72
Removing idle function -1
Refinement elapsed time: 0.045
INFO:: backup file coot-backup/Fitted_ligand_#4-0_Mon_May_14_11:47:02_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.684 and 8 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -197.7
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 53) at -406.3
Final Estimated RMS Z Scores:
bonds: 0.3424
angles: 0.338
torsions: N/A
planes: 0.4979
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 37.64
Removing idle function -1
Refinement elapsed time: 0.042
INFO:: backup file coot-backup/Fitted_ligand_#5-0_Mon_May_14_11:47:03_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.096 and 8 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -159.2
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 6) at -256
Final Estimated RMS Z Scores:
bonds: 0.1705
angles: 0.1232
torsions: N/A
planes: 0.3314
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 38.54
Removing idle function -1
Refinement elapsed time: 0.033
INFO:: backup file coot-backup/Fitted_ligand_#6-0_Mon_May_14_11:47:04_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.636 and 8 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -94.09
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 11) at -561.5
Final Estimated RMS Z Scores:
bonds: 0.2971
angles: 0.3288
torsions: N/A
planes: 0.2755
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 39.5
Removing idle function -1
Refinement elapsed time: 0.097
INFO:: backup file coot-backup/Fitted_ligand_#7-0_Mon_May_14_11:47:05_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.07 and 3 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -150
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 9) at -322
Final Estimated RMS Z Scores:
bonds: 0.4698
angles: 0.4951
torsions: N/A
planes: 0.1658
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 39.91
Removing idle function -1
Refinement elapsed time: 0.061
INFO:: backup file coot-backup/Fitted_ligand_#8-0_Mon_May_14_11:47:05_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.857 and 5 are decent out of 12
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
created 39 restraints
INFO:: make_restraints(): made 58 non-bonded restraints
initial distortion_score: -122.5
Initial RMS Z values
bonds: 2.322
angles: 0.02556
torsions: N/A
planes: 0.02599
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 6) at -224.6
Final Estimated RMS Z Scores:
bonds: 0.1073
angles: 0.0365
torsions: N/A
planes: 0.2375
non-bonded: 0
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 40.47
Removing idle function -1
Refinement elapsed time: 0.02
INFO:: backup file coot-backup/Fitted_ligand_#9-0_Mon_May_14_11:47:06_2018_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
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
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 133 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_May_14_11:47:07_2018_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_May_14_11:47:07_2018_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_May_14_11:47:07_2018_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Mon_May_14_11:47:07_2018_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: Reading coordinate file: /home/paule/data/greg-data/dipole-residues.pdb
PDB file /home/paule/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
Model 1 had 0 links
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 135 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/home/paule/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/paule/data/greg-data/libcheck_3GP.cif had no bond restraints
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 136 read successfully
DEBUG:: there were 0 types with no dictionary
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 136
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 136
INFO:: Reading coordinate file: /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb
PDB file /home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 137 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.029 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.002 seconds for statistics
Map mean: ........ 1.041e-09
Map sigma: ....... 0.3115
Map maximum: ..... 2.978
Map minimum: ..... -0.875
INFO:: 0.012 seconds for contour map
INFO:: 0.063 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 137
Sequence: ?EYTVITPGARTR
Confidence: 1
From : HEYTVITPGARTR
Chain id: 0 Offset: 53
INFO:: backup file coot-backup/_home_paule_data_greg-data_crashes_on_cootaneering-v2.pdb_Mon_May_14_11:47:09_2018_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:: thrown Null previous residue
WARNING:: no rotamers probabilities for residue type GLY
INFO:: replace_coords: 12 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: 15 atoms updated.
INFO:: replace_coords: 10 atoms updated.
INFO:: replace_coords: 10 atoms updated.
INFO:: replace_coords: 11 atoms updated.
INFO:: replace_coords: 10 atoms updated.
INFO:: replace_coords: 10 atoms updated.
WARNING:: thrown Failed to get a good fitting result
WARNING:: no rotamers probabilities for residue type GLY
WARNING:: thrown Failed to get a good fitting result
WARNING:: no rotamers probabilities for residue type ALA
INFO:: replace_coords: 14 atoms updated.
INFO:: replace_coords: 10 atoms updated.
WARNING:: thrown Null next residue
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
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 0/8
INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_May_14_11:47:09_2018_modification_0.pdb.gz
INFO:: Matching/moving molecule number 141 to 141
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_Mon_May_14_11:47:09_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| 1, 0.003218, -0.003497|
| -0.003225, 1, -0.001985|
| 0.003491, 0.001997, 1|
( -24.05, -23.7, -24.44)
No unit cell for this molecule, hence no fractional matrix.
INFO:: Reading coordinate file: /home/paule/data/greg-data/1wly.pdb
PDB file /home/paule/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
Molecule 142 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/1yb5.pdb
PDB file /home/paule/data/greg-data/1yb5.pdb has been read.
Spacegroup: P 21 21 2
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
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 143 read successfully
DEBUG:: there were 2 types with no dictionary
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: reference 142 has 750 atoms selected
INFO:: moving 143 has 842 atoms selected
superposing...
number of Ca atoms in selections: 110 (moving) and 100 (reference)
Another Go...
Moving Reference Distance(/A)
A 6
A 7
A 8 <---> A 2 : 0.7510
A 9 <---> A 3 : 0.9422
A 10 <---> A 4 : 0.6300
A 11 <---> A 5 : 0.7119
A 12 <---> A 6 : 0.6310
A 13 <---> A 7 : 0.4675
A 14 <---> A 8 : 0.4264
A 15 <---> A 9 : 0.9792
A 16 <---> A 10 : 0.7549
A 17 <---> A 11 : 0.4884
A 18 <---> A 12 : 0.7451
A 19 <---> A 13 : 0.4606
A 20 <---> A 14 : 1.2809
A 21 <---> A 15 : 1.2412
A 22 <---> A 16 : 1.0733
A 23 <---> A 17 : 0.9730
A 24 <---> A 18 : 0.4705
A 25 <---> A 19 : 0.3560
A 26 <---> A 20 : 3.1145
A 27
A 28 <---> A 21 : 1.5754
A 29 <---> A 22 : 1.6322
A 30
A 31 <---> A 23 : 1.9973
A 32 <---> A 25 : 1.8324
A 33 <---> A 26 : 0.9310
A 34 <---> A 27 : 0.6808
A 35 <---> A 28 : 0.2674
A 36 <---> A 29 : 0.5995
A 37 <---> A 30 : 0.6992
A 38 <---> A 31 : 0.8620
A 39 <---> A 32 : 0.8421
A 40 <---> A 33 : 0.7208
A 41 <---> A 34 : 0.8681
A 42 <---> A 35 : 0.7781
A 43 <---> A 36 : 0.6211
A 44 <---> A 37 : 0.4657
A 45 <---> A 38 : 0.7475
A 46 <---> A 39 : 0.5170
A 47 <---> A 40 : 0.5058
A 48 <---> A 41 : 0.8897
A 49 <---> A 42 : 0.5835
A 50 <---> A 43 : 0.4347
A 51 <---> A 44 : 0.6192
A 52 <---> A 45 : 0.2150
A 53 <---> A 46 : 0.7474
A 54 <---> A 47 : 1.0213
A 55 <---> A 48 : 0.9208
A 56 <---> A 49 : 0.9392
A 57
A 58
A 59
A 60
A 61
A 62
A 63
A 64
A 65 <---> A 60 : 0.4666
A 66 <---> A 61 : 0.0523
A 67 <---> A 62 : 1.0719
A 68 <---> A 63 : 0.7933
A 69 <---> A 64 : 0.8916
A 70 <---> A 65 : 1.2580
A 71 <---> A 66 : 0.6932
A 72 <---> A 67 : 1.0345
A 73 <---> A 68 : 1.4417
A 74 <---> A 69 : 0.9092
A 75 <---> A 70 : 1.6166
A 76 <---> A 71 : 0.8741
A 77 <---> A 72 : 0.2388
A 78 <---> A 73 : 0.3118
A 79 <---> A 74 : 0.3887
A 80 <---> A 75 : 0.7613
A 81 <---> A 76 : 0.9044
A 82 <---> A 77 : 0.6090
A 83 <---> A 78 : 1.7978
A 84 <---> A 79 : 1.9256
A 85 <---> A 80 : 1.3416
A 86 <---> A 81 : 0.5658
A 87 <---> A 82 : 0.4480
A 88 <---> A 83 : 0.9078
A 89 <---> A 84 : 0.3625
A 90 <---> A 85 : 0.4040
A 91 <---> A 86 : 0.4586
A 92 <---> A 87 : 0.4340
A 93 <---> A 88 : 0.3664
A 94 <---> A 89 : 0.4921
A 95 <---> A 90 : 0.6498
A 96 <---> A 91 : 1.5805
A 97 <---> A 92 : 2.8839
A 98
A 99
A 100
Moving: KLMRAVRVFEFGGPEVLKLRSDIAVPIPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVAG
Target: --VMAAVIHKKGGPDNFVWEE-VK-VSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAAA
Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY
Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI
INFO:: backup file coot-backup/_home_paule_data_greg-data_1yb5.pdb_Mon_May_14_11:47:10_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| -0.9117, -0.3803, 0.1557|
| -0.3625, 0.9227, 0.131|
| -0.1935, 0.06299, -0.9791|
( 70.65, 7.793, 21.29)
Rotation - polar (omega,phi,kappa) 87.1413 101.0220 169.7385
Rotation - euler (alpha,beta,gamma) 40.0716 168.2570 18.0277
Translation - Angstroms 70.6538 7.7930 21.2852
.0065 0.325 2.711 0.904 0.030
: 140 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.711 0.904 0.030
: 141 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.710 0.903 0.030
: 142 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.710 0.903 0.030
: 143 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.709 0.903 0.030
: 144 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.709 0.903 0.030
: 145 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.709 0.903 0.030
: 146 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.708 0.903 0.030
: 147 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.708 0.903 0.030
: 148 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.707 0.902 0.030
: 149 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.707 0.902 0.030
: 150 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.707 0.902 0.030
: 151 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.706 0.902 0.030
: 152 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.706 0.902 0.030
: 153 0.0 0.0 0.0 0. 0.0 0.0065 0.325 2.706 0.902 0.030
: 154 0.0 0.0 0.0 0. 0.0 0.0065 0.324 2.705 0.902 0.030
: 155 0.0 0.0 0.0 0. 0.0 0.0065 0.324 2.705 0.902 0.030
: 156 0.0 0.0 0.0 0. 0.0 0.0065 0.324 2.705 0.902 0.030
: 157 0.0 0.0 0.0 0. 0.0 0.0065 0.324 2.704 0.901 0.030
: 158 0.0 0.0 0.0 0. 0.0 0.0065 0.324 2.704 0.901 0.030
: 159 0.0 0.0 0.0 0. 0.0 0.0065 0.324 2.703 0.901 0.030
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
: Refmac_5.8.0073: End of Refmac_5.8.0073
:Times: User: 3.0s 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: 4.15699248796084
distance d2: 1.49011611938477e-7
PASS: flip residue (around eigen vectors)
Entered testcase - Test dipole
info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0)
PASS: Test dipole
Entered testcase - Reading new dictionary restraints replaces
PASS: Reading new dictionary restraints replaces
Entered testcase - Pyrogen Runs OK?
PASS: Pyrogen Runs OK?
Entered testcase - pyrogen dictionary does not make double-quoted atom names
PASS: pyrogen dictionary does not make double-quoted atom names
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 137 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 - AINFO: core rmsd achieved: 1.0199 Angstroems
number of residues in reference structure: 322
number of residues in moving structure: 324
number of residues in aligned sections (reference): 100
number of residues in aligned sections (moving): 110
number of aligned residues: 95
number of gaps: 4
number of misdirections: 0
number of SSE combinations: 4.0000
sequence identity: 30.5263%
WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb
lice Dawson's Example
0 "/home/paule/data/greg-data/tutorial-modern.pdb"
2 "/home/paule/data/greg-data/ins-code-fragment-pre.pdb"
3 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
4 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
5 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
6 "test-3hfl.map"
7 "/home/paule/data/greg-data/tutorial-modern.pdb"
8 "mainchain"
9 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb"
10 "atom selection from tutorial-add-terminal-1-test.pdb"
11 "/home/paule/data/greg-data/frag-2wot.pdb"
12 "sphere selection from tutorial-modern.pdb"
14 "/home/paule/data/greg-data/rotamer-test-fragment.pdb"
15 "/home/paule/data/greg-data/res098.pdb"
16 "/home/paule/data/greg-data/tutorial-modern.pdb"
17 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
18 "/home/paule/data/greg-data/pdb3knw.ent"
19 "/home/paule/data/greg-data/pdb1py3.ent"
22 "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb"
23 "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb"
24 "/home/paule/data/greg-data/tutorial-modern.pdb"
25 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
26 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb"
27 "/home/paule/data/greg-data/tutorial-modern.pdb"
28 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
29 "/home/paule/data/greg-data/tutorial-modern.pdb"
30 "/home/paule/data/greg-data/alt-conf-waters.pdb"
31 "/home/paule/data/greg-data/backrub-fragment.pdb"
32 "Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb"
33 "/home/paule/data/greg-data/coords-B3A.pdb"
34 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT"
35 "/home/paule/data/greg-data/test-TER-OXT.pdb"
36 "/home/paule/data/greg-data/val.pdb"
37 "/home/paule/data/greg-data/2yie-frag.pdb"
38 "/home/paule/data/greg-data/4f8g.pdb"
39 "/home/paule/data/greg-data/4f8g.pdb"
40 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
41 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
42 "/home/paule/data/greg-data/tutorial-modern.pdb"
43 "Generic Masked Map"
44 "difference-map"
47 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
48 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
49 "averaged-map"
50 "difference-map"
51 "/home/paule/data/greg-data/multi-carbo-coot-3.pdb"
52 "/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb"
53 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
54 "/home/paule/data/greg-data/monomer-VAL.pdb"
55 "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb"
56 "atom selection from tutorial-modern.pdb"
57 "/home/paule/data/greg-data/monomer-ACT.pdb"
58 "/home/paule/data/greg-data/tutorial-modern.pdb"
59 "/home/paule/data/greg-data/tutorial-modern.pdb"
60 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
61 "atom selection from tutorial-modern.pdb"
62 "/home/paule/data/greg-data/tutorial-modern.pdb"
63 "/home/paule/data/greg-data/tutorial-modern.pdb"
64 "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb"
65 "/home/paule/data/greg-data/tutorial-modern.pdb"
66 "/home/paule/data/greg-data/tutorial-modern.pdb"
67 "/home/paule/data/greg-data/pdb3hfl.ent"
68 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
69 "Ideal-A-form-RNA"
70 "Ideal-A-form-RNA"
71 "Ideal-A-form-DNA"
72 "Ideal-A-form-DNA"
73 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
74 "/home/paule/data/greg-data/some-waters-with-ter.pdb"
75 "/home/paule/data/greg-data/tm+some-waters.pdb"
76 "/home/paule/data/INFO:: Reading coordinate file: /home/paule/data/greg-data/2qd9.pdb
PDB file /home/paule/data/greg-data/2qd9.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
Molecule 144 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: Reading coordinate file: /home/paule/data/greg-data/2gtn.pdb
PDB file /home/paule/data/greg-data/2gtn.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
INFO:: NCS chain comparison 0/337
Molecule 145 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: reference 144 has 169 atoms selected
INFO:: moving 145 has 169 atoms selected
superposing...
number of Ca atoms in selections: 21 (moving) and 21 (reference)
Another Go...
Moving Reference Distance(/A)
A 140 <---> A 140 : 0.1804
A 141 <---> A 141 : 0.0760
A 142 <---> A 142 : 0.1052
A 143 <---> A 143 : 0.1246
A 144 <---> A 144 : 0.1370
A 145 <---> A 145 : 0.1380
A 146 <---> A 146 : 0.1662
A 147 <---> A 147 : 0.2744
A 148 <---> A 148 : 0.2728
A 149 <---> A 149 : 0.1173
A 150 <---> A 150 : 0.1684
A 151 <---> A 151 : 0.0928
A 152 <---> A 152 : 0.1200
A 153 <---> A 153 : 0.1281
A 154 <---> A 154 : 0.2539
A 155 <---> A 155 : 0.6351
A 156 <---> A 156 : 0.1300
A 157 <---> A 157 : 0.1478
A 158 <---> A 158 : 0.2238
A 159 <---> A 159 : 0.2271
A 160 <---> A 160 : 0.2372
Moving: YIHSADIIHRDLKPSNLAVNE
Target: YIHSADIIHRDLKPSNLAVNE
INFO:: backup file coot-backup/_home_paule_data_greg-data_2gtn.pdb_Mon_May_14_11:47:11_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| 0.9998, 0.009845, -0.01938|
| -0.009814, 1, 0.001689|
| 0.0194, -0.001498, 0.9998|
( 0.3207, 0.6598, 0.8819)
Rotation - polar (omega,phi,kappa) 116.8035 -94.6984 1.2491
Rotation - euler (alpha,beta,gamma) 175.0200 1.1149 -175.5832
Translation - Angstroms 0.3207 0.6598 0.8819
INFO: core rmsd achieved: 0.2210 Angstroems
number of residues in reference structure: 330
number of residues in moving structure: 337
number of residues in aligned sections (reference): 21
number of residues in aligned sections (moving): 21
number of aligned residues: 21
number of gaps: 0
number of misdirections: 0
number of SSE combinations: 1.0000
sequence identity: 100.0000%
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O S
INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000
READ-INS:: Spacegroup: "I 21 3"
INFO:: read_file() chain with chain id has 121 residues
Symmetry available for this molecule
Molecule 146 read successfully
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0290 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0200 seconds for FFT
INFO:: 0.0020 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 2.9776
Map minimum: ..... -0.8750
INFO:: 0.0130 seconds for contour map
INFO:: 0.0640 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 147 NCS found from matching Chain B onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
| 0.9637, -0.07462, -0.2563|
| 0.2651, 0.3804, 0.886|
| 0.0314, -0.9218, 0.3864|
( 38.09, -17.87, 14.32)
inverse of reference matcher transformation:
| 0.9637, 0.2651, 0.0314|
| -0.07462, 0.3804, -0.9218|
| -0.2563, 0.886, 0.3864|
( -32.42, 22.84, 20.06)
boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985)
INFO:: There were 2.0000 maps contributing to the average
INFO:: rescaling by 0.5000
INFO:: 228096 out of 228096 (100.0000%) map points were masked out of NCS average target volume, chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: 0.0004 st.d: 0.3236
Map statistics: min: -1.4496, max: 2.3411
-1.4022 3
-1.3074 1
-1.2127 4
-1.1179 8
-1.0231 5
-0.9283 32
-0.8336 104
-0.7388 349
-0.6440 1163
-0.5493 3433
-0.4545 8783
-0.3597 17620
-0.2650 27133
-0.1702 32345
-0.0754 31462
0.0193 26827
0.1141 20587
0.2089 15419
0.3036 11965
0.3984 8787
0.4932 6637
0.5879 4777
0.6827 3343
0.7775 2426
0.8722 1733
0.9670 1142
1.0618 796
1.1565 469
1.2513 296
1.3461 188
1.4409 96
1.5356 80
1.6304 34
1.7252 20
1.8199 14
1.9147 6
2.0095 4
2.1042 3
2.1990 0
2.2938 2
2.3885 0
no diffs
NCS target chain has 93 peers.
INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb
PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
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 152 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:47:12_2018_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:47:12_2018_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:47:12_2018_modification_2.pdb.gz
INFO:: NCS chain comparison 90/93
First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100
INFO:: LSQ matched 90 atoms
INFO:: 90 matched atoms had:
mean devi: 0.3643
rms devi: 0.4571
max devi: 2.1351
min devi: 0.0881
find_ncs_matrix returns (LSQ)
| 0.9705, -0.04634, -0.2366|
| 0.2357, 0.3884, 0.8908|
| 0.05061, -0.9203, 0.3878|
( 37.8, -17.18, 13.82)
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 152 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 152 and ichain: 0
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 0
Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 90/93
First atom of 720 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 724 in second selection 1/B/4 {GLY}/ N altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100
INFO:: LSQ matched 90 atoms
INFO:: 90 matched atoms had:
mean devi: 0.3643
rms devi: 0.4571
max devi: 2.1351
min devi: 0.0881
find_ncs_matrix returns (LSQ)
| 0.9705, -0.04634, -0.2366|
| 0.2357, 0.3884, 0.8908|
| 0.05061, -0.9203, 0.3878|
( 37.8, -17.18, 13.82)
Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:47:12_2018_modification_3.pdb.gz
INFO:: mutate 2 A to a TRP
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:47:12_2018_modification_4.pdb.gz
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 152 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 152 and ichain: 0
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 0
Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 92/93
First atom of 727 in first selection 1/A/1 {ASP}/ N altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 745 in second selection 1/B/1 {ASP}/ N altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700
INFO:: LSQ matched 93 atoms
INFO:: 93 matched atoms had:
mean devi: 0.3427
rms devi: 0.4454
max devi: 2.1352
min devi: 0.0124
find_ncs_matrix returns (LSQ)
| 0.9705, -0.04643, -0.2365|
| 0.2356, 0.3891, 0.8906|
| 0.05068, -0.92, 0.3886|
( 37.8, -17.17, 13.81)
Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_May_14_11:47:12_2018_modification_5.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1t6q.ent
PDB file /home/paule/data/greg-data/pdb1t6q.ent has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 2 biomt matrices
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 153 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: mutate 50 A to a ASP
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_May_14_11:47:13_2018_modification_0.pdb.gz
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2048
rms devi: 0.2651
max devi: 1.1707
min devi: 0.0160
find_ncs_matrix returns (LSQ)
| 0.5407, 0.4775, 0.6926|
| -0.4862, -0.4944, 0.7205|
| 0.6865, -0.7263, -0.03511|
( -28.15, 65.89, 42.9)
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2275
rms devi: 0.3035
max devi: 1.6549
min devi: 0.0661
find_ncs_matrix returns (LSQ)
| 0.5303, -0.4851, 0.6953|
| 0.4758, -0.5085, -0.7177|
| 0.7017, 0.7114, -0.03884|
( 18.19, 77.78, -25.69)
INFO:: fill_ghost_info Constructed 2 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 153 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 153 and ichain: 0
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 0
Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 893 in second selection 1/B/6 {CYS}/ N altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2048
rms devi: 0.2651
max devi: 1.1707
min devi: 0.0160
find_ncs_matrix returns (LSQ)
| 0.5407, 0.4775, 0.6926|
| -0.4862, -0.4944, 0.7205|
| 0.6865, -0.7263, -0.03511|
( -28.15, 65.89, 42.9)
Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first selection 1/A/7 {GLY}/ N altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 881 in second selection 1/C/7 {GLY}/ N altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had:
mean devi: 0.2275
rms devi: 0.3035
max devi: 1.6549
min devi: 0.0661
find_ncs_matrix returns (LSQ)
| 0.5303, -0.4851, 0.6953|
| 0.4758, -0.5085, -0.7177|
| 0.7017, 0.7114, -0.03884|
( 18.19, 77.78, -25.69)
Adding ghost with name: NCS found from matching Chain C onto Chain A
INFO:: set_ncs_master_chain Constructed 2 ghosts
Ghost info:: NCS found from matching Chain B onto Chain A
Ghost info:: NCS found from matching Chain C onto Chain A
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_May_14_11:47:13_2018_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_May_14_11:47:13_2018_modification_2.pdb.gz
INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent
PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
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 154 read successfully
DEBUG:: there were 0 types with no dictionary
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 154 and chain_id: B
%%%%%% add_ncs_ghosts_using_ncs_master
%%%%%% imaster: 1
Checking chains for NCS matching to chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 540 in second selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had:
mean devi: 2.4989
rms devi: 2.7962
max devi: 6.6860
min devi: 0.4401
find_ncs_matrix returns (LSQ)
| 0.7026, 0.1278, 0.7|
| 0.6024, 0.4169, -0.6807|
| -0.3788, 0.8999, 0.2159|
( 62.25, -87.53, -9.128)
Adding ghost with name: NCS found from matching Chain A onto Chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had:
mean devi: 2.6728
rms devi: 2.9369
max devi: 6.1200
min devi: 0.2483
find_ncs_matrix returns (LSQ)
| -0.3504, -0.8022, -0.4834|
| -0.7587, -0.05952, 0.6488|
| -0.5492, 0.594, -0.5878|
( -29.05, 14.61, -72.53)
Adding ghost with name: NCS found from matching Chain C onto Chain B
INFO:: NCS chain comparison 61/62
First atom of 506 in first selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had:
mean devi: 1.7317
rms devi: 1.9769
max devi: 7.9453
min devi: 0.5297
find_ncs_matrix returns (LSQ)
| -0.3815, -0.9208, -0.08098|
| -0.9191, 0.3685, 0.1396|
| -0.09874, 0.1277, -0.9869|
( -11.18, 4.757, -127.2)
Adding ghost with name: NCS found from matching Chain D onto Chain B
INFO:: NCS chain comparison 0/62
INFO:: set_ncs_master_chain Constructed 3 ghosts
Ghost info:: NCS found from matching Chain A onto Chain B
Ghost info:: NCS found from matching Chain C onto Chain B
Ghost info:: NCS found from matching Chain D onto Chain B
INFO:: Matching/moving molecule number 155 to 154
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had:
mean devi: 0.2239
rms devi: 0.2350
max devi: 0.3369
min devi: 0.0588
INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925)
INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426)
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Mon_May_14_11:47:14_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| 0.3395, 0.5177, 0.7853|
| 0.8624, 0.162, -0.4796|
| -0.3755, 0.8401, -0.3915|
( 90.55, -91.12, -47.52)
INFO:: fractional coordinates matrix:
| 0.8374, 0.1106, 0.6656|
| 0.9958, -0.3359, -0.7249|
| -0.2868, 0.6992, -0.3915|
( 0.4296, -1.191, -0.411)
INFO:: Matching/moving molecule number 156 to 154
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had:
mean devi: 0.1943
rms devi: 0.2112
max devi: 0.3583
min devi: 0.0329
INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095)
INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905)
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Mon_May_14_11:47:14_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| -0.6203, -0.2279, -0.7505|
| -0.4559, -0.6739, 0.5814|
| -0.6382, 0.7028, 0.3141|
( -22.14, -19.93, 1.626)
INFO:: fractional coordinates matrix:
| -0.8835, -0.09252, -0.543|
| -0.5264, -0.4107, 0.8789|
| -0.4875, 0.7087, 0.3141|
( -0.381, -0.2605, 0.01406)
INFO:: Matching/moving molecule number 157 to 154
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had:
mean devi: 0.4174
rms devi: 0.4531
max devi: 0.7926
min devi: 0.0759
INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411)
INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232)
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_pdb1hvv.ent_Mon_May_14_11:47:14_2018_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| -0.2227, -0.9733, -0.05471|
| -0.9662, 0.2129, 0.1454|
| -0.1299, 0.08525, -0.9879|
( -15.82, -0.3228, -130)
INFO:: fractional coordinates matrix:
| -0.7806, -0.3462, 0.03831|
| -1.116, 0.7707, 0.2198|
| -0.09924, 0.106, -0.9879|
( -0.1813, -0.00422, -1.125)
greg-data/tutorial-modern.pdb"
77 "/home/paule/data/greg-data/water-test-no-cell.pdb"
78 "/home/paule/data/greg-data/pathological-water-test.pdb"
79 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
80 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
81 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
82 "/home/paule/data/greg-data/tutorial-modern.pdb"
83 "/home/paule/data/greg-data/pdb1hvv.ent"
84 "/home/paule/data/greg-data/monomer-ACT.pdb"
85 "/home/paule/data/greg-data/monomer-NPO.pdb"
86 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_83"
87 "/home/paule/data/greg-data/tutorial-modern.pdb"
88 "atom selection from tutorial-modern.pdb"
89 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
90 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
91 "/home/paule/data/greg-data/tutorial-modern.pdb"
92 "/home/paule/data/greg-data/pdb1py3.ent"
93 "/home/paule/data/greg-data/tutorial-modern.pdb"
94 "/home/paule/data/greg-data/tutorial-modern.pdb"
95 "/home/paule/data/greg-data/2goz-manip.pdb"
96 "/home/paule/data/greg-data/tutorial-modern.pdb"
97 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
98 "/home/paule/data/greg-data/HOF.RES"
99 "/home/paule/data/greg-data/hollander.ins"
102 "/home/paule/data/greg-data/insulin.fcf Diff-SigmaA"
103 "atom selection from insulin.res"
104 "atom selection from insulin.res"
106 "/home/paule/data/greg-data/horma-p21.res"
107 "new-horma.ins"
108 "/home/paule/data/greg-data/crash.hat"
109 "coot-ccp4/monomer-3GP.pdb"
110 "/home/paule/data/greg-data/monomer-3GP.pdb"
111 "/home/paule/data/greg-data/test-LIG.pdb"
112 "/home/paule/data/greg-data/test-LIG.pdb"
113 "/home/paule/data/greg-data/monomer-NPO.pdb"
114 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
115 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
116 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
117 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
118 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
119 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb"
120 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT"
121 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT"
122 "Masked (by protein)"
123 "Fitted ligand #0-0"
124 "Fitted ligand #1-0"
125 "Fitted ligand #2-0"
126 "Fitted ligand #3-0"
127 "Fitted ligand #4-0"
128 "Fitted ligand #5-0"
129 "Fitted ligand #6-0"
130 "Fitted ligand #7-0"
131 "Fitted ligand #8-0"
132 "Fitted ligand #9-0"
133 "coot-ccp4/monomer-3GP.pdb"
134 "Copy_of_coot-ccp4/monomer-3GP.pdb"
135 "/home/paule/data/greg-data/dipole-residues.pdb"
136 "/home/paule/data/greg-data/tutorial-modern.pdb"
137 "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb"
138 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
139 "Ideal-A-form-RNA"
142 "/home/paule/data/greg-data/1wly.pdb"
143 "/home/paule/data/greg-data/1yb5.pdb"
PASS: SSM - Alice Dawson's Example
Entered testcase - SSM by atom selection [JED Example]
PASS: SSM by atom selection [JED Example]
Ended 06-ssm.scm
Running 07-ncs.scm ...
Entered testcase - NCS maps test
PASS: NCS maps test
Entered testcase - NCS chains info
NCS info: (("A" "B"))
PASS: NCS chains info
Entered testcase - NCS deviation info
PASS: NCS deviation info
Entered testcase - NCS Residue Range copy
PASS: NCS Residue Range copy
Entered testcase - NCS Residue Range edit to all chains
result: (#t #t)
PASS: NCS Residue Range edit to all chains
Entered testcase - Manual NCS ghosts generates correct NCS chain ids
NCS ghost chain IDs pre: (("B" "A" "C" "D"))
NCS ghost chain IDs post: (("B" "A" "C" "D"))
PASS: Manual NCS ghosts generates correct NCS chain INFO:: Reading coordinate file: /home/paule/data/greg-data/pdb1hvv.ent
PDB file /home/paule/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
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 158 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/1hvv_sigmaa.mtz
Number of OBSERVED reflections: 20903
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 112, 112, 150)
INFO:: 0.0360 seconds to read MTZ file
INFO:: 0.0210 seconds to initialize map
INFO:: 0.0330 seconds for FFT
INFO:: 0.0030 seconds for statistics
Map mean: ........ -0.0000
Map sigma: ....... 0.2241
Map maximum: ..... 1.7219
Map minimum: ..... -0.8818
INFO:: 0.0070 seconds for contour map
INFO:: 0.1000 seconds in total
INFO:: NCS chain comparison 62/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had:
mean devi: 2.4989
rms devi: 2.7962
max devi: 6.6860
min devi: 0.4401
find_ncs_matrix returns (LSQ)
| 0.7026, 0.6024, -0.3788|
| 0.1278, 0.4169, 0.8999|
| 0.7, -0.6807, 0.2159|
( 5.528, 36.75, -101.2)
INFO:: NCS chain comparison 66/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 66 atoms
INFO:: 66 matched atoms had:
mean devi: 1.9713
rms devi: 2.1729
max devi: 4.5411
min devi: 0.4295
find_ncs_matrix returns (LSQ)
| -0.4445, -0.8903, -0.09887|
| -0.893, 0.4317, 0.1271|
| -0.07049, 0.1448, -0.9869|
( -8.624, 7.402, -127.7)
INFO:: NCS chain comparison 61/67
First atom of 540 in first selection 1/A/190 {GLN}/ N altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had:
mean devi: 3.7042
rms devi: 4.0859
max devi: 9.4383
min devi: 0.2858
find_ncs_matrix returns (LSQ)
| -0.7198, -0.6079, 0.3353|
| -0.5986, 0.2989, -0.7432|
| 0.3516, -0.7356, -0.579|
( 36.14, -61.4, -149.3)
INFO:: NCS chain comparison 0/67
INFO:: fill_ghost_info Constructed 3 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Ghost 2 name: "NCS found from matching Chain D onto Chain A"
INFO:: installing ghost map with name :Map 159 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 159 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 159 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 159 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 159 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 159 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 159 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 159 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 159 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: /home/paule/data/greg-data/monomer-ACT.pdb
PDB file /home/paule/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
Molecule 168 read successfully
DEBUG:: there were 0 types with no dictionary
Entering test: OXT in restraints?
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/
There are 135 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/A.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/C.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/G.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/u/U.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HOH.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/n/NA.cif
There are 2 data in /home/paule/data/greg-data/libcheck_BCS.cif
PASS: OXT in restraints?
Entering test: Relative file name
PASS: Relative file name
Entering test: geometry distortion comparision
Good gdi < exception thrown
Good gdi > exception thrown
PASS: geometry distortion comparision
Entering test: test symm trans to origin
Got length 0.1414
PASS: test symm trans to origin
Entering test: test lsq plane
LSQ deviations: 0.0000 0.0000
PASS: test lsq plane
Entering test: test COO modification
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/
There are 135 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/a/A.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/c/C.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/g/G.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/u/U.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/h/HOH.cif
There are 2 data in /home/paule/ccp4/ccp4-6.4.0/lib/data/monomers/n/NA.cif
INFO:: Reading coordinate file: /home/paule/data/greg-data/hideous-OXT.pdb
PDB file /home/paule/data/greg-data/hideous-OXT.pdb has been read.
Spacegroup: P 21 21 21
read 9 atom
created 7 bond restraints
created 8 angle restraints
created 1 plane restraints
created 1 chiral vol restraints
created 2 torsion restraints
created 23 restraints
INFO:: make_restraints(): made 13 non-bonded restraints
initial distortion_score: 1241.5407
Initial RMS Z values
bonds: 3.7208
angles: 7.4688
torsions: 0.2764
planes: 16.9011
non-bonded: 0.0000
chiral vol: 1.2266
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 243) at 0.0349
Final Estimated RMS Z Scores:
bonds: 0.0017
angles: 0.0239
torsions: 0.1205
planes: 0.0019
non-bonded: 0.0000
chiral vol: 0.0068
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
refinement_took 0.0050 seconds
OXT out of plane distance: 0.0000
OXT->O distance: 2.1104
PASS: test COO modification
Entering test: remove whitespace
PASS: remove whitespace
Entering test: New comp_ids are sane
PASS: New comp_ids are sane
Entering test: Remove Trailing Slash
PASS: Remove Trailing Slash
Entering test: Residues for phi,psi are close enough to be considered linked
INFO:: Reading coordinate file: /home/paule/data/greg-data/frag-2wot.pdb
PDB file /home/paule/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
bad residues for phi,psi calculation
bad residues for phi,psi calculation
PASS: Residues for phi,psi are close enough to be considered linked
ids
Entered testcase - NCS maps overwrite existing maps
==== test-name: "Map 159 NCS found from matching Chain B onto Chain A" n-matchers: 2
==== test-name: "Map 159 NCS found from matching Chain C onto Chain A" n-matchers: 2
==== test-name: "Map 159 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 125
# of expected passes 125
# 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 125
# of expected passes 125
# of expected failures 0
# of unexpected passes 0
# of unexpected failures 0
# of unresolved testcases 0
# of unsupported testcases 0
# of untested testcases 0
# of files abandoned 0
ObjectCache: Leaked 0002 refs to <P 2ac 2ab Nuvw = ( 108, 132, 64)>
ObjectCache: Leaked 0004 refs to <C 2c 2 Nuvw = ( 160, 160, 336)>
ObjectCache: Leaked 0002 refs to <P 2ac 2ab>
ObjectCache: Leaked 0004 refs to <C 2c 2>
test_coot: coot test passed