testing with greg
testing with greg
currently we are here:
/home/paule/autobuild/building/emsley-vm-debian-7-7_2019-04-01__T10_36_02/coot-0.8.9.2-pre
Mon 1 Apr 12:12:11 BST 2019
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 Afternoon Paul, Welcome to Coot version 0.8.9.2-pre
[1m(set-display-intro-string "Good Afternoon Paul, Welcome to Coot version 0.8.9.2-pre")[0m
[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 afternoon 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.
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_Apr__1_12:12:43_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_Apr__1_12:12:43_2019_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Mon_Apr__1_12:12:43_2019_modification_2.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 3 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_1.pdb.gz
INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_2.pdb.gz
INFO:: Matching/moving molecule number 4 to 3
INFO:: LSQ matched 15 atoms
INFO:: 15 matched atoms had:
mean devi: 0.605779
rms devi: 0.634415
max devi: 0.938213
min devi: 0.391381
INFO:: Axis orientation: ( -0.5848, -0.7505, 0.3079)
INFO:: Rotation in CCP4 Polar Angles: Polar = (72.0654,-127.924,156.99)
INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_3.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| -0.2638, 0.7224, -0.6392|
| 0.9632, 0.1612, -0.2152|
| -0.05243, -0.6724, -0.7383|
( 69.15, -27.17, 32.75)
No unit cell for this molecule, hence no fractional matrix.
INFO:: backup file coot-backup/PTR_from_dict_Mon_Apr__1_12:12:43_2019_modification_4.pdb.gz
INFO:: match.MatchGraphs must match at least 9 atoms.
INFO:: match NumberofMatches (potentially similar graphs) 2
WARNING:: in torsion match() quad moving not all non-blank
------ after matching, check the torsions
torsion check: ( N CA CB CG ) was -60.01 should be -47.18 and is -47.18
torsion check: ( CA CB CG CD2) was -90.31 should be -56.84 and is -56.84
INFO:: rotated 2 torsions in matching torsions
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:12:43_2019_modification_0.pdb.gz
------- resulting_merge_info has size 1
-------- resulting_merge_info[0] [spec: 1 "A" 101 ""]
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:12:43_2019_modification_1.pdb.gz
INFO:: created 40 restraints
created 16 bond restraints
created 22 angle restraints
created 1 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
6 angle links
4 plane links
1 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 610 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 55734.43
Initial RMS Z values
bonds: 8.93
angles: 9.45
torsions: N/A
planes: 12.49
non-bonded: 83.62
chiral vol: 0.26
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 61) at 60.39
Final Estimated RMS Z Scores:
bonds: 0.42
angles: 1.33
torsions: N/A
planes: 0.57
non-bonded: 0.00
chiral vol: 2.27
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 0.00
debug:: restraints results 1 5
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:12:43_2019_modification_2.pdb.gz
INFO:: replace_coords: 16 atoms updated.
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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.50
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 22.18 seconds to read MTZ file
INFO:: 0.01 seconds to initialize map
INFO:: 2.15 seconds for FFT
INFO:: 0.00 seconds for statistics
Map mean: ........ 0.00
Map sigma: ....... 0.31
Map maximum: ..... 2.98
Map minimum: ..... -0.88
INFO:: 0.00 seconds for contour map
INFO:: 24.34 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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.50
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.03 seconds to read MTZ file
INFO:: 0.00 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.00 seconds for statistics
Map mean: ........ 0.00
Map sigma: ....... 0.31
Map maximum: ..... 2.98
Map minimum: ..... -0.88
INFO:: 0.00 seconds for contour map
INFO:: 0.05 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz
INFO:: Number of observed reflections: 17920
INFO:: finding ASU unique map points with sampling rate 1.50
INFO:: grid sampling...Nuvw = ( 64, 96, 90)
INFO:: 8.25 seconds to read MTZ file
INFO:: 0.08 seconds to initialize map
INFO:: 0.02 seconds for FFT
INFO:: 0.00 seconds for statistics
Map mean: ........ 0.00
Map sigma: ....... 0.26
Map maximum: ..... 1.72
Map minimum: ..... -1.03
INFO:: 0.00 seconds for contour map
INFO:: 8.35 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: 0.00 st.d: 0.26
Map statistics: min: -1.03, max: 1.72
-1.00 1
-0.93 8
-0.86 23
-0.79 96
-0.72 305
-0.66 714
-0.59 1587
-0.52 2927
-0.45 5202
-0.38 7937
-0.31 11655
-0.24 16895
-0.17 24542
-0.11 34962
-0.04 43098
0.03 41219
0.10 29087
0.17 15906
0.24 8720
0.31 6095
0.38 4870
0.45 4308
0.51 3717
0.58 3304
0.65 2688
0.72 2065
0.79 1620
0.86 1097
0.93 786
1.00 479
1.06 257
1.13 146
1.20 73
1.27 35
1.34 20
1.41 14
1.48 11
1.55 7
1.61 3
1.68 1
1.75 0
INFO:: n grid points: 276480
INFO:: mean before filtering: 0.00
INFO:: variance before filtering: 0.07
INFO:: filter by ignoring 210 of 276480 counts ( = 0.0760%) with values around -0.0054 from bin 3737 of 10000
Map mean: ........ 0.0000
Map rmsd: ........ 0.2605
Map maximum: ..... 1.7179
Map minimum: ..... -1.0339
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 9 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
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
142 fragments garnered from /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
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
Adding fragments from: /home/paule/autobuild/Linux-emsley-vm-debian-7-7-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
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
not backwards A contains 94 residues from 1 to 93
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-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 11 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:08_2019_modification_0.pdb.gz
not backwards A contains 114 residues from -19 to 93
target fragment start res: -19 had 0 db fragment hits, ilength=6
retrying with ilength = 5 produces 14 hits.
2nd part with ilength = 5, iresno=-18 produces 9 hits.
target fragment start res: -16 had 22 db fragment hits, ilength=6
target fragment start res: -13 had 48 db fragment hits, ilength=6
target fragment start res: -10 had 29 db fragment hits, ilength=6
target fragment start res: -7 had 1772 db fragment hits, ilength=6
target fragment start res: -4 had 2040 db fragment hits, ilength=6
target fragment start res: -1 had 2021 db fragment hits, ilength=6
breaking out of match_target_fragment 6 with iresno= 2
merge fragments -19 to 6 with 8 fit sets to merge
The merging is complete
mainchain_fragment from -19 to 6
done mainchain_fragment
successfully set cell and symmetry
short target_ca 0 with iresno 10, trying 9
short target_ca 0 with iresno 9, trying 8
WARNING:: short target at start - bailing out now.
merge fragments 10 to 30 with 0 fit sets to merge
The merging is complete
mainchain_fragment from 10 to 30
done mainchain_fragment
(process:4654): Gtk-CRITICAL **: IA__gtk_widget_show: assertion `GTK_IS_WIDGET (widget)' failed
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 13 read successfully
DEBUG:: there were 0 types with no dictionary
fitting terminal residue with 5000 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_Apr__1_12:15:09_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:09_2019_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 15 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276
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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0190 seconds for FFT
INFO:: 0.0030 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 2.9776
Map minimum: ..... -0.8750
INFO:: 0.0010 seconds for contour map
INFO:: 0.0520 seconds in total
fitting terminal residue with 5000 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/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:09_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:09_2019_modification_1.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:09_2019_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 20 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 ""]
WARNING:: Error reading /home/paule/data/greg-data/eleanor-HIS.pdb
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 21 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: created 19 restraints
created 10 bond restraints
created 8 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
7 angle links
5 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 129 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 599.3325
Initial RMS Z values
bonds: 0.1989
angles: 0.4071
torsions: N/A
planes: 0.5035
non-bonded: 4.4321
chiral vol: 0.1627
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 239) at 9.9937
Final Estimated RMS Z Scores:
bonds: 0.0729
angles: 0.6197
torsions: N/A
planes: 0.5967
non-bonded: 0.0000
chiral vol: 0.5924
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 146.2020
debug:: restraints results 1 5
INFO:: backup file coot-backup/_home_paule_data_greg-data_res098.pdb_Mon_Apr__1_12:15:10_2019_modification_0.pdb.gz
INFO:: replace_coords: 11 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 22 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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0190 seconds for FFT
INFO:: 0.0030 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 2.9776
Map minimum: ..... -0.8750
INFO:: 0.0000 seconds for contour map
INFO:: 0.0510 seconds in total
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:10_2019_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! -------------------
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:10_2019_modification_1.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 11.7495
Good afternoon 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 - Replace Residue gets correct residue number
debug:: in overlap-by-main-chain:: ---------------- imol-mov: 4 imol-ref: 3
DEBUG:: ------ new-chain-id-info: (1 ((#t "A" 101 "")))
DEBUG:: ------ merge-status: 1
debug:: ------ new-res-spec: (#t "A" 101 "")
debug:: ------ change-residue-number to 86
debug:: ------ chain ids : "A" "A"
C-N dist good enough: 1.33591012485164
PASS: Replace Residue gets correct residue number
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 - Negative Residues in db-mainchain don't cause a crash
PASS: Negative Residues in db-mainchain don't cause a crash
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 - Add Terminal Residue O Position
Add terminal residue bond check dd-1: 0.14997610541894
Add terminal residue bond check dd-2: 2.25586252670689
PASS: Add Terminal Residue O Position
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 - HIS with unusual atom order rotates correct fragment for 180 sidechain flip
BAD imol for 180 sidechain flip test imol: -1
FAIL: HIS with unusual atom order rotates correct fragment for 180 sidechain flip
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-fitINFO:: 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 24 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3knw.ent_Mon_Apr__1_12:15:10_2019_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 25 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_Apr__1_12:15:11_2019_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
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 26 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
INFO:: 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:: 0.0190 seconds for FFT
INFO:: 0.0030 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 2.9776
Map minimum: ..... -0.8750
INFO:: 0.0010 seconds for contour map
INFO:: 0.0520 seconds in total
DEBUG:: split_residue table
0 N ::
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_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 28 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_Apr__1_12:15:11_2019_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 29 read successfully
DEBUG:: there were 0 types with no dictionary
omega: 1 12.7704 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_Apr__1_12:15:11_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_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_Apr__1_12:15:11_2019_modification_2.pdb.gz
INFO:: created 21 restraints
created 10 bond restraints
created 10 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
1 bond links
4 angle links
3 plane links
1 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
7 angle links
5 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 138 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 4781.3414
Initial RMS Z values
bonds: 15.4585
angles: 7.1242
torsions: N/A
planes: 1.8999
non-bonded: 29.0131
chiral vol: 3.0446
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 38) at -4775.0334
Final Estimated RMS Z Scores:
bonds: 0.9643
angles: 0.7789
torsions: N/A
planes: 2.3214
non-bonded: 0.0431
chiral vol: 0.1157
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 147.1530
Refinement elapsed time: 0.0130
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_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_Apr__1_12:15:11_2019_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_modification_5.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 8.4516
INFO:: created 32 restraints
created 14 bond restraints
created 16 angle restraints
created 0 plane restraints
created 2 chiral vol restraints
Link restraints:
1 bond links
4 angle links
3 plane links
1 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
2 bond links
7 angle links
5 plane links
2 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 222 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -5899.3677
Initial RMS Z values
bonds: 0.9474
angles: 1.6100
torsions: N/A
planes: 2.8722
non-bonded: 0.1736
chiral vol: 0.4224
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 3) at -6027.2788
Final Estimated RMS Z Scores:
bonds: 0.9354
angles: 0.6993
torsions: N/A
planes: 2.3820
non-bonded: 0.0289
chiral vol: 0.1238
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 147.2330
Refinement elapsed time: 0.0120
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Mon_Apr__1_12:15:11_2019_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 30 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz
cliquize 12 spinables for altconf
--------------------------- 12 cliques ----------------
omega: 1 -177.7480 degrees
INFO This is a TRANS peptide - making it CIS
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 32 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz
cliquize 11 spinables for altconf
--------------------------- 10 cliques ----------------
3 ---
[spec: model 1 "A" 6 "" " CG1" ""]
[spec: model 1 "A" 11 "" " CD2" ""]
INFO:: mutate 10 A to a GLY
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_modification_1.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 34 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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 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:: 0.0010 seconds for contour map
INFO:: 0.0510 seconds in total
INFO:: created 11 restraints
created 6 bond restraints
created 4 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 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 80 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -3168.4874
Initial RMS Z values
bonds: 2.0711
angles: 1.0696
torsions: N/A
planes: 0.6113
non-bonded: 3.4160
chiral vol: 1.4620
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 64) at -3413.0046
Final Estimated RMS Z Scores:
bonds: 1.1108
angles: 1.5126
torsions: N/A
planes: 0.2626
non-bonded: 0.3751
chiral vol: 1.2342
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 147.4210
Refinement elapsed time: 0.0060
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:11_2019_modification_0.pdb.gz
INFO:: replace_coords: 7 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 36 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_Apr__1_12:15:11_2019_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: -15654.1423
Initial RMS Z values
bonds: 1.7426
angles: 1.2676
torsions: N/A
planes: 0.8383
non-bonded: 0.0007
chiral vol: 0.8944
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 27) at -16041.7470
Final Estimated RMS Z Scores:
bonds: 1.0091
angles: 0.6518
torsions: N/A
planes: 0.5835
non-bonded: 0.0000
chiral vol: 0.2404
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 147.5380
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:11_2019_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: -7143.5789
Initial RMS Z values
bonds: 0.9807
angles: 1.0175
torsions: N/A
planes: 1.7875
non-bonded: 5.2955
chiral vol: 10.2816
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 58) at -15651.6817
Final Estimated RMS Z Scores:
bonds: 1.9471
angles: 1.7856
torsions: N/A
planes: 1.6126
non-bonded: 0.0500
chiral vol: 1.7692
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 147.6490
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-add-terminal-1-test.pdb_Mon_Apr__1_12:15:11_2019_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 37 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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0190 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:: 0.0010 seconds for contour map
INFO:: 0.0510 seconds in total
INFO:: created 67 restraints
created 29 bond restraints
created 32 angle restraints
created 2 plane restraints
created 4 chiral vol restraints
Link restraints:
3 bond links
9 angle links
6 plane links
2 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 868 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -3041.7182
Initial RMS Z values
bonds: 0.9358
angles: 1.0580
torsions: N/A
planes: 1.9846
non-bonded: 7.4770
chiral vol: 11.4845
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 1) at -11414.3979
Final Estimated RMS Z Scores:
bonds: 2.0037
angles: 1.9678
torsions: N/A
planes: 1.7242
non-bonded: 0.0604
chiral vol: 2.0928
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 147.8120
Refinement elapsed time: 0.0630
----------------------------------------------
----------------------------------------------
ERROR:: A: last_restraints no cleared up
----------------------------------------------
----------------------------------------------
INFO:: created 67 restraints
created 29 bond restraints
created 32 angle restraints
created 2 plane restraints
created 4 chiral vol restraints
Link restraints:
3 bond links
9 angle links
6 plane links
2 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 868 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 4868.0924
Initial RMS Z values
bonds: 0.9358
angles: 1.0580
torsions: N/A
planes: 1.9846
non-bonded: 7.4770
chiral vol: 11.4845
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 75) at -2825.8990
Final Estimated RMS Z Scores:
bonds: 0.8192
angles: 1.3983
torsions: N/A
planes: 1.8356
non-bonded: 0.0188
chiral vol: 1.2862
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 147.9010
Refinement elapsed time: 0.0890
----------------------------------------------
----------------------------------------------
ERROR:: A: last_restraints no cleared up
----------------------------------------------
----------------------------------------------
INFO:: created 67 restraints
created 29 bond restraints
created 32 angle restraints
created 2 plane restraints
created 4 chiral vol restraints
Link restraints:
3 bond links
9 angle links
6 plane links
2 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 868 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 6111.3710
Initial RMS Z values
bonds: 0.9358
angles: 1.0580
torsions: N/A
planes: 1.9846
non-bonded: 7.4770
chiral vol: 11.4845
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 73) at -1514.1070
Final Estimated RMS Z Scores:
bonds: 0.6156
angles: 1.2624
torsions: N/A
planes: 1.8069
non-bonded: 0.0116
chiral vol: 1.0780
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 148.0140
Refinement elapsed time: 0.1120
----------------------------------------------
----------------------------------------------
ERROR:: A: last_restraints no cleared up
----------------------------------------------
----------------------------------------------
INFO:: created 67 restraints
created 29 bond restraints
created 32 angle restraints
created 2 plane restraints
created 4 chiral vol restraints
Link restraints:
3 bond links
9 angle links
6 plane links
2 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 868 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 6580.0776
Initial RMS Z values
bonds: 0.9358
angles: 1.0580
torsions: N/A
planes: 1.9846
non-bonded: 7.4770
chiral vol: 11.4845
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 5) at -1026.8395
Final Estimated RMS Z Scores:
bonds: 0.5241
angles: 1.1747
torsions: N/A
planes: 1.7905
non-bonded: 0.0085
chiral vol: 0.9902
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 148.2010
Refinement elapsed time: 0.1870
----------------------------------------------
----------------------------------------------
ERROR:: A: last_restraints no cleared up
----------------------------------------------
----------------------------------------------
INFO:: created 67 restraints
created 29 bond restraints
created 32 angle restraints
created 2 plane restraints
created 4 chiral vol restraints
Link restraints:
3 bond links
9 angle links
6 plane links
2 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 868 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 6807.3837
Initial RMS Z values
bonds: 0.9358
angles: 1.0580
torsions: N/A
planes: 1.9846
non-bonded: 7.4770
chiral vol: 11.4845
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 58) at -793.2879
Final Estimated RMS Z Scores:
bonds: 0.4709
angles: 1.1159
torsions: N/A
planes: 1.7831
non-bonded: 0.0070
chiral vol: 0.9340
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 148.4380
Refinement elapsed time: 0.2360
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 39 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: -1086.3897
Initial RMS Z values
bonds: 1.6203
angles: 1.0091
torsions: N/A
planes: 0.7374
non-bonded: 0.0256
chiral vol: 0.5795
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 35) at -1239.1218
Final Estimated RMS Z Scores:
bonds: 0.1620
angles: 0.5206
torsions: N/A
planes: 0.3319
non-bonded: 0.0023
chiral vol: 0.2772
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 148.5080
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:12_2019_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
PASS: Correction of CISPEP test
Entered testcase - H on a N moves on cis-trans convert
dd: 3.29414331487717
PASS: H on a N moves on cis-trans convert
Entered testcase - HA on a ALA exists after mutation to GLY
PASS: HA on a ALA exists after mutation to GLY
Entered testcase - Refine Zone with Alt conf
refined moved: d=0.170920995733268
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: 2.004" 2.00372433662415) ("Angles" "Angles: 1.968" 1.96783602237701) ("Planes" "Planes: 1.724" 1.72420871257782) ("Non-bonded" "Non-bonded: 0.246" 0.245682418346405) ("Chirals" "Chirals: 2.093" 2.09279537200928)))
ow factor: 1.94714111089706
INFO:: setting refinement weight to 15.825462010273
refinement results: ("" 0 (("Bonds" "Bonds: 0.819" 0.819224894046783) ("Angles" "Angles: 1.398" 1.39832580089569) ("Planes" "Planes: 1.836" 1.83556282520294) ("Non-bonded" "Non-bonded: 0.137" 0.137185722589493) ("Chirals" "Chirals: 1.286" 1.28615963459015)))
ow factor: 1.33481828868389
INFO:: setting refinement weight to 8.88202742880352
refinement results: ("" 0 (("Bonds" "Bonds: 0.616" 0.615578889846802) ("Angles" "Angles: 1.262" 1.26242864131927) ("Planes" "Planes: 1.807" 1.8069269657135) ("Non-bonded" "Non-bonded: 0.108" 0.107924073934555) ("Chirals" "Chirals: 1.078" 1.07801687717438)))
ow factor: 1.19073784351349
INFO:: setting refinement weight to 6.26440470144893
refinement results: ("" 0 (("Bonds" "Bonds: 0.524" 0.524065494537354) ("Angles" "Angles: 1.175" 1.17469692230225) ("Planes" "Planes: 1.791" 1.79053711891174) ("Non-bonded" "Non-bonded: 0.092" 0.0923675745725632) ("Chirals" "Chirals: 0.990" 0.990249395370483)))
ow factor: 1.11988723278046
INFO:: setting refinement weight to 4.99495091490859
refinement results: ("" 0 (("Bonds" "Bonds: 0.471" 0.470898509025574) ("Angles" "Angles: 1.116" 1.1158994436264) ("Planes" "Planes: 1.783" 1.78314650058746) ("Non-bonded" "Non-bonded: 0.084" 0.0838774889707565) ("Chirals" "Chirals: 0.934" 0.93397319316864)))
ow factor: 1.07597941160202
PASS: Refinement gives useful results
Entered testcase - Neighbour-Refine doesn't destroy disulfide bonds
bond-length-within-tolerance? bond-length 2.03286102466317 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.5975971221924 27.5079345703125 11.2516946792603)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7325477600098 27.0097732543945 9.48080539703369))
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: -1239.1218
Initial RMS Z values
bonds: 0.1620
angles: 0.5206
torsions: N/A
planes: 0.3319
non-bonded: 0.0023
chiral vol: 0.2772
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 1) at -1239.1230
Final Estimated RMS Z Scores:
bonds: 0.1610
angles: 0.5205
torsions: N/A
planes: 0.3321
non-bonded: 0.0023
chiral vol: 0.2790
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 148.5330
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:15:12_2019_modification_1.pdb.gz
INFO:: replace_coords: 27 atoms updated.
bond-length-within-tolerance? bond-length 2.03298326695991 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.597599029541 27.5079555511475 11.2517795562744)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7326126098633 27.0097522735596 9.48073101043701))
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 40 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_Apr__1_12:15:13_2019_modification_0.pdb.gz
INFO:: replace_coords: 1 atoms updated.
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
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 41 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_Apr__1_12:15:13_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_backrub-fragment.pdb_Mon_Apr__1_12:15:13_2019_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 43 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: created 11 restraints
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 5 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 2.9511
Initial RMS Z values
bonds: 0.6619
angles: 0.3737
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.2500
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 23) at 0.0000
Final Estimated RMS Z Scores:
bonds: 0.0014
angles: 0.0027
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.0012
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 148.8480
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_Apr__1_12:15:13_2019_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
INFO:: created 11 restraints
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 5 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 0.0000
Initial RMS Z values
bonds: 0.0014
angles: 0.0027
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.0012
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 1) at 0.0000
Final Estimated RMS Z Scores:
bonds: 0.0003
angles: 0.0026
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.0007
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 148.9580
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_Apr__1_12:15:13_2019_modification_1.pdb.gz
INFO:: replace_coords: 6 atoms updated.
Welcome to Coot
INFO:: created 11 restraints
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 5 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 3.0185
Initial RMS Z values
bonds: 0.6708
angles: 0.3753
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.2536
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 16) at 0.0000
Final Estimated RMS Z Scores:
bonds: 0.0004
angles: 0.0004
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.0002
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 149.0760
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_coords-B3A.pdb_Mon_Apr__1_12:15:13_2019_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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0190 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:: 0.0010 seconds for contour map
INFO:: 0.0510 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.
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 45 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_Apr__1_12:15:13_2019_modification_0.pdb.gz
Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.0897,14.9163) B-factor: 45.0000
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.
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 46 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_Apr__1_12:15:13_2019_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.
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 47 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_2yie-frag.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz
INFO:: 6 matched atoms had:
mean devi: 0.0404
rms devi: 0.0472
max devi: 0.0833
min devi: 0.0130
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 48 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz
INFO:: 6 matched atoms had:
mean devi: 0.0435
rms devi: 0.0478
max devi: 0.0740
min devi: 0.0148
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 49 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_4f8g.pdb_Mon_Apr__1_12:15:13_2019_modification_0.pdb.gz
INFO:: 6 matched atoms had:
mean devi: 0.0394
rms devi: 0.0445
max devi: 0.0695
min devi: 0.0151
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0300 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:: 0.0000 seconds for contour map
INFO:: 0.0520 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.2000
INFO:: grid sampling...Nuvw = ( 160, 192, 96)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0330 seconds to initialize map
INFO:: 0.0390 seconds for FFT
INFO:: 0.0060 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 3.0518
Map minimum: ..... -0.9217
INFO:: 0.0010 seconds for contour map
INFO:: 0.1070 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 52 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: Masking around 64 atoms
Map statistics: mean: -0.0014 st.d: 0.3056
Map statistics: min: -0.8750, max: 2.9776
-0.8269 9
-0.7306 46
-0.6343 403
-0.5379 2065
-0.4416 7564
-0.3453 17348
-0.2490 26177
-0.1527 33633
-0.0564 40439
0.0400 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
1.0031 1314
1.0994 958
1.1957 645
1.2921 455
1.3884 271
1.4847 175
1.5810 108
1.6773 59
1.7736 34
1.8699 17
1.9663 7
2.0626 2
2.1589 1
2.2552 4
2.3515 1
2.4478 0
2.5442 1
2.6405 0
2.7368 0
2.8331 0
2.9294 0
3.0257 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: -0.0014 st.d: 0.0601
Map statistics: min: -2.7883, max: 0.7305
-2.7443 1
-2.6564 1
-2.5684 1
-2.4804 1
-2.3925 1
-2.3045 1
-2.2165 0
-2.1285 1
-2.0406 0
-1.9526 3
-1.8646 1
-1.7767 1
-1.6887 5
-1.6007 3
-1.5128 4
-1.4248 6
-1.3368 21
-1.2488 16
-1.1609 41
-1.0729 35
-0.9849 54
-0.8970 68
-0.8090 85
-0.7210 108
-0.6331 116
-0.5451 145
-0.4571 148
-0.3692 181
-0.2812 209
-0.1932 264
-0.1052 356
-0.0173 223669
0.0707 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 55 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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0190 seconds for FFT
INFO:: 0.0030 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 2.9776
Map minimum: ..... -0.8750
INFO:: 0.0000 seconds for contour map
INFO:: 0.0510 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 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:: 0.0010 seconds for contour map
INFO:: 0.0510 seconds in total
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.5000
INFO:: grid sampling...Nuvw = ( 180, 216, 108)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0450 seconds to initialize map
INFO:: 0.0510 seconds for FFT
INFO:: 0.0090 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 3.0713
Map minimum: ..... -0.8775
INFO:: 0.0020 seconds for contour map
INFO:: 0.1350 seconds in total
INFO:: multiplying map (function index) 0 Nuvw = ( 108, 132, 64) by 1.0000
INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1.0000
Map statistics: mean: -0.0000 st.d: 0.3111
Map statistics: min: -0.8734, max: 2.9750
-0.8253 9
-0.7291 49
-0.6328 422
-0.5366 2147
-0.4404 7837
-0.3442 17839
-0.2480 26781
-0.1518 34418
-0.0556 41152
0.0406 36651
0.1368 21808
0.2330 10320
0.3293 5945
0.4255 4553
0.5217 3766
0.6179 3294
0.7141 2796
0.8103 2261
0.9065 1818
1.0027 1374
1.0989 984
1.1951 684
1.2914 472
1.3876 284
1.4838 182
1.5800 106
1.6762 63
1.7724 39
1.8686 15
1.9648 10
2.0610 2
2.1572 2
2.2535 5
2.3497 2
2.4459 1
2.5421 2
2.6383 1
2.7345 0
2.8307 1
2.9269 0
3.0231 1
Map statistics: mean: 0.0000 st.d: 0.0011
Map statistics: min: -0.0069, max: 0.0119
-0.0066 5
-0.0062 21
-0.0057 31
-0.0052 53
-0.0047 114
-0.0043 221
-0.0038 460
-0.0033 817
-0.0029 1522
-0.0024 2764
-0.0019 4797
-0.0015 9242
-0.0010 19273
-0.0005 40373
-0.0000 61229
0.0004 44297
0.0009 20929
0.0014 9475
0.0018 4785
0.0023 2778
0.0028 1678
0.0032 1172
0.0037 689
0.0042 491
0.0046 288
0.0051 198
0.0056 151
0.0061 102
0.0065 56
0.0070 37
0.0075 18
0.0079 10
0.0084 10
0.0089 3
0.0093 1
0.0098 3
0.0103 2
0.0108 0
0.0112 0
0.0117 0
0.0122 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 61 read successfully
DEBUG:: there were 2 types with no dictionary
INFO:: created 138 restraints
created 46 bond restraints
created 82 angle restraints
created 2 plane restraints
created 8 chiral vol restraints
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
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 799 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 2651.7158
Initial RMS Z values
bonds: 6.1616
angles: 2.8528
torsions: N/A
planes: 0.0835
non-bonded: 0.2115
chiral vol: 0.9035
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 887) at 15.9904
Final Estimated RMS Z Scores:
bonds: 0.1009
angles: 0.4225
torsions: N/A
planes: 0.0264
non-bonded: 0.0002
chiral vol: 0.1561
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 150.8740
debug:: restraints results 1 5
INFO:: backup file coot-backup/_home_paule_data_greg-data_multi-carbo-coot-3.pdb_Mon_Apr__1_12:15:15_2019_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 1/110
Molecule 62 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
INFO:: 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:: 0.0010 seconds for contour map
INFO:: 0.0520 seconds in total
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
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 64 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: found bad VAL chiral atom: A 1 CB
INFO:: created 40 restraints
created 14 bond restraints
created 25 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 44 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 4.9970
Initial RMS Z values
bonds: 0.5425
angles: 0.1641
torsions: N/A
planes: N/A
non-bonded: 0.0000
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: 0.0122
angles: 0.0949
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.1454
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 195.9980
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: undo molecule number set to: 64
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_1.pdb.gz
restoring from backup 2 2
INFO:: Reading coordinate file: coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz
PDB file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_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
INFO:: created 40 restraints
created 14 bond restraints
created 25 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 44 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 4.9970
Initial RMS Z values
bonds: 0.5425
angles: 0.1641
torsions: N/A
planes: N/A
non-bonded: 0.0000
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: 0.0122
angles: 0.0949
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.1454
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 196.0670
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-VAL.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
PASS: Make a glycosidic linkage
Entered testcase - Refine an NAG-ASN Link
Exception: (missing-atom-1)
UNRESOLVED: 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.
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 65 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: created 49 restraints
created 17 bond restraints
created 31 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 67 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 903.0633
Initial RMS Z values
bonds: 5.6211
angles: 3.4330
torsions: N/A
planes: N/A
non-bonded: 0.0000
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: 0.0094
angles: 0.1210
torsions: N/A
planes: N/A
non-bonded: 0.0000
chiral vol: 0.1385
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 196.1170
debug:: restraints results 1 4
INFO:: backup file coot-backup/_home_paule_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Mon_Apr__1_12:16:00_2019_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))
INFO:: created 28 restraints
created 11 bond restraints
created 15 angle restraints
created 1 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 40 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 2873.4804
Initial RMS Z values
bonds: 1.1515
angles: 0.8476
torsions: N/A
planes: 3.0558
non-bonded: 79.8585
chiral vol: 0.7578
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 50) at -324.3456
Final Estimated RMS Z Scores:
bonds: 0.2820
angles: 0.2076
torsions: N/A
planes: 0.1840
non-bonded: 0.0090
chiral vol: 0.0522
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 196.1730
Refinement elapsed time: 0.0120
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_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: 2.62799378529819:
bond-length-within-tolerance? bond-length 2.62799378529819 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.2963485717773 4.44178247451782 19.7638034820557)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.524772644043 6.66353750228882 19.08473777771))
INFO:: created 29 restraints
created 12 bond restraints
created 15 angle restraints
created 1 plane restraints
created 1 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 39 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 2248.5321
Initial RMS Z values
bonds: 14.6461
angles: 0.2076
torsions: N/A
planes: 0.1840
non-bonded: 0.0000
chiral vol: 0.0522
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 58) at -355.5101
Final Estimated RMS Z Scores:
bonds: 0.0864
angles: 0.1256
torsions: N/A
planes: 0.2928
non-bonded: 0.0000
chiral vol: 0.0627
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 196.1940
Refinement elapsed time: 0.0120
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_1.pdb.gz
INFO:: replace_coords: 12 atoms updated.
pass intermediate 2.8 tolerance test
OK plane atom " CB "
Bond-length: 1.51471268369434:
bond-length-within-tolerance? bond-length 1.51471268369434 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5267486572266 4.8825421333313 19.387336730957)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.2792510986328 6.16372489929199 19.0929470062256))
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 67 read successfully
DEBUG:: there were 1 types with no dictionary
Welcome to Coot
WARNING:: bond_restraint_length 4 should be 5
INFO:: created 15 restraints
created 5 bond restraints
created 9 angle restraints
created 1 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 7 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 4835.2158
Initial RMS Z values
bonds: 0.0120
angles: 0.0065
torsions: N/A
planes: 0.0000
non-bonded: 689.9273
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 45) at -87.3139
Final Estimated RMS Z Scores:
bonds: 0.0158
angles: 0.1325
torsions: N/A
planes: 0.0141
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 196.4270
Refinement elapsed time: 0.0330
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-ACT.pdb_Mon_Apr__1_12:16:00_2019_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 68 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_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_Apr__1_12:16:00_2019_modification_2.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_3.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_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_Apr__1_12:16:00_2019_modification_6.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:00_2019_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 69 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_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: (44.8780,12.9550,8.7610) 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:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:01_2019_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 72 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_Apr__1_12:16:01_2019_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 73 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44.0000%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33.0000%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13.0000%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.0000%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9.0000%]
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 74 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: aligning to mol number 74 chain: A
----- input to align_on_chain() -----------------
chain A
target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
wgap -3.0000
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 150.0000
DEBUG:: s.length() 95
DEBUG:: nSelResidues 87
INFO:: backup file coot-backup/_home_paule_data_greg-data_rnase-A-needs-an-insertion.pdb_Mon_Apr__1_12:16:02_2019_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: 138874360 "A" 1 ""] -> ASP
[spec: 138874360 "A" 2 ""] -> VAL
[spec: 138874360 "A" 3 ""] -> SER
[spec: 138874360 "A" 11 ""] -> LEU
[spec: 138874360 "A" 12 ""] -> PRO
[spec: 138874360 "A" 13 ""] -> PRO
[spec: 138874360 "A" 62 ""] -> PRO
[spec: 138874360 "A" 63 ""] -> GLY
Deletions:
[spec: 138874360 "A" 25 ""]
[spec: 138874360 "A" 34 ""]
Mutations:
[spec: 138874360 "A" 24 ""] -> SER
[spec: 138874360 "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 75 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:02_2019_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 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_Apr__1_12:16:02_2019_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.
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 77 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz
INFO:: Number of observed reflections: 17920
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 64, 96, 90)
INFO:: 0.0220 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0140 seconds for FFT
INFO:: 0.0020 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.2604
Map maximum: ..... 1.7179
Map minimum: ..... -1.0339
INFO:: 0.0010 seconds for contour map
INFO:: 0.0390 seconds in total
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Fitting score for best rotamer: 5.8340
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb3hfl.ent_Mon_Apr__1_12:16:05_2019_modification_1.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.0000
rms devi: 0.0000
max devi: 0.0000
min devi: 0.0000
INFO:: 5 matched atoms had:
mean devi: 0.0121
rms devi: 0.0134
max devi: 0.0214
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.2702
rms devi: 0.3350
max devi: 0.5360
min devi: 0.0846
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: 0.3350
max devi: 0.5360
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: 0.0120
rms devi: 0.0133
max devi: 0.0213
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.0002
rms devi: 0.0002
max devi: 0.0003
min devi: 0.0002
INFO:: 5 matched atoms had:
mean devi: 0.2702
rms devi: 0.3350
max devi: 0.5360
min devi: 0.0846
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: 0.0001
rms devi: 0.0001
max devi: 0.0001
min devi: 0.0001
INFO:: 5 matched atoms had:
mean devi: 0.0120
rms devi: 0.0134
max devi: 0.0214
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.0001
rms devi: 0.0001
max devi: 0.0001
min devi: 0.0001
INFO:: 5 matched atoms had:
mean devi: 0.0120
rms devi: 0.0134
max devi: 0.0213
min devi: 0.0039
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: 0.0848
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_Apr__1_12:16:05_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Apr__1_12:16:05_2019_modification_1.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.2690
rms devi: 0.3372
max devi: 0.5475
min devi: 0.0818
INFO:: 5 matched atoms had:
mean devi: 0.0000
rms devi: 0.0000
max devi: 0.0000
min devi: 0.0000
INFO:: 5 matched atoms had:
mean devi: 0.0121
rms devi: 0.0134
max devi: 0.0214
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.2702
rms devi: 0.3350
max devi: 0.5360
min devi: 0.0846
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: 0.3350
max devi: 0.5360
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: 0.0120
rms devi: 0.0133
max devi: 0.0213
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.0002
rms devi: 0.0002
max devi: 0.0003
min devi: 0.0002
INFO:: 5 matched atoms had:
mean devi: 0.2702
rms devi: 0.3350
max devi: 0.5360
min devi: 0.0846
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: 0.0001
rms devi: 0.0001
max devi: 0.0001
min devi: 0.0001
INFO:: 5 matched atoms had:
mean devi: 0.0120
rms devi: 0.0134
max devi: 0.0214
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.0001
rms devi: 0.0001
max devi: 0.0001
min devi: 0.0001
INFO:: 5 matched atoms had:
mean devi: 0.0120
rms devi: 0.0134
max devi: 0.0213
min devi: 0.0039
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: 0.0848
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_Apr__1_12:16:05_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Mon_Apr__1_12:16:05_2019_modification_1.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.2690
rms devi: 0.3372
max devi: 0.5475
min devi: 0.0818
INFO:: 5 matched atoms had:
mean devi: 0.0059
rms devi: 0.0067
max devi: 0.0101
min devi: 0.0026
INFO:: 5 matched atoms had:
mean devi: 0.0073
rms devi: 0.0078
max devi: 0.0126
min devi: 0.0046
INFO:: 5 matched atoms had:
mean devi: 0.2718
rms devi: 0.3364
max devi: 0.5338
min devi: 0.0878
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: 0.0072
rms devi: 0.0077
max devi: 0.0124
min devi: 0.0046
INFO:: 5 matched atoms had:
mean devi: 0.0057
rms devi: 0.0066
max devi: 0.0100
min devi: 0.0024
INFO:: 5 matched atoms had:
mean devi: 0.2718
rms devi: 0.3364
max devi: 0.5338
min devi: 0.0878
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: 0.0059
rms devi: 0.0067
max devi: 0.0101
min devi: 0.0025
INFO:: 5 matched atoms had:
mean devi: 0.0072
rms devi: 0.0078
max devi: 0.0125
min devi: 0.0046
INFO:: 5 matched atoms had:
mean devi: 0.0058
rms devi: 0.0066
max devi: 0.0100
min devi: 0.0025
INFO:: 5 matched atoms had:
mean devi: 0.0072
rms devi: 0.0077
max devi: 0.0124
min devi: 0.0046
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: 0.0880
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_Apr__1_12:16:05_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_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_Apr__1_12:16:05_2019_modification_2.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.2719
rms devi: 0.3363
max devi: 0.5345
min devi: 0.0923
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_modification_3.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.0043
rms devi: 0.0048
max devi: 0.0074
min devi: 0.0019
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_modification_4.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.2657
rms devi: 0.3260
max devi: 0.5019
min devi: 0.0927
INFO:: 5 matched atoms had:
mean devi: 0.0059
rms devi: 0.0067
max devi: 0.0101
min devi: 0.0026
INFO:: 5 matched atoms had:
mean devi: 0.0073
rms devi: 0.0078
max devi: 0.0126
min devi: 0.0046
INFO:: 5 matched atoms had:
mean devi: 0.2718
rms devi: 0.3364
max devi: 0.5338
min devi: 0.0878
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: 0.0072
rms devi: 0.0077
max devi: 0.0124
min devi: 0.0046
INFO:: 5 matched atoms had:
mean devi: 0.0057
rms devi: 0.0066
max devi: 0.0100
min devi: 0.0024
INFO:: 5 matched atoms had:
mean devi: 0.2718
rms devi: 0.3364
max devi: 0.5338
min devi: 0.0878
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: 0.0059
rms devi: 0.0067
max devi: 0.0101
min devi: 0.0025
INFO:: 5 matched atoms had:
mean devi: 0.0072
rms devi: 0.0078
max devi: 0.0125
min devi: 0.0046
INFO:: 5 matched atoms had:
mean devi: 0.0058
rms devi: 0.0066
max devi: 0.0100
min devi: 0.0025
INFO:: 5 matched atoms had:
mean devi: 0.0072
rms devi: 0.0077
max devi: 0.0124
min devi: 0.0046
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: 0.0880
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_Apr__1_12:16:05_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_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_Apr__1_12:16:05_2019_modification_2.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.2719
rms devi: 0.3363
max devi: 0.5345
min devi: 0.0923
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_modification_3.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.0043
rms devi: 0.0048
max devi: 0.0074
min devi: 0.0019
INFO:: backup file coot-backup/Ideal-A-form-DNA_Mon_Apr__1_12:16:05_2019_modification_4.pdb.gz
INFO:: 5 matched atoms had:
mean devi: 0.2657
rms devi: 0.3260
max devi: 0.5019
min devi: 0.0927
INFO:: mutate 32 A to a LYS
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_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.
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 84 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_Apr__1_12:16:05_2019_modification_0.pdb.gz
1/D/79 {HOH}/ O altLoc :: segid :: pos: (3.0000,4.0000,5.0000) B-factor: 45.0000 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 85 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 2.0000
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.3115
INFO:: Using density cut-off: 0.6230 (2.0000 sigma) (mean -0.0337 stdev: 0.1461)
INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4000 3.2000
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_Apr__1_12:16:05_2019_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 86 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_0.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_1.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_2.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_3.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_4.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_5.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_6.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_7.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_8.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_9.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_10.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_11.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_12.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_13.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_14.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_15.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_16.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_17.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_18.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_19.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_20.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_21.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_22.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_23.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_24.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_25.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_26.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_27.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_28.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_29.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_30.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_31.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_32.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_33.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_34.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_35.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_36.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_37.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_38.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_39.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_40.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_41.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_42.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_43.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_44.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_45.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_46.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_47.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_48.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_49.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_50.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_51.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_52.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_53.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_54.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_55.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_56.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_57.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_58.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_59.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_60.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_61.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_62.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_63.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_64.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_65.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_66.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_67.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_68.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_69.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_70.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_71.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_72.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_73.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_74.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_75.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_76.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_77.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_78.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_79.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_80.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_81.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_82.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_83.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_84.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_85.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_86.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_87.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_88.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_89.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_90.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_91.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_92.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_93.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_94.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_95.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_96.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_97.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_98.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:05_2019_modification_99.pdb.gz
0//-32767 {MG}/MG altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 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.
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 87 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_Apr__1_12:16:07_2019_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 88 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_Apr__1_12:16:08_2019_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
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 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:: 0.0010 seconds for contour map
INFO:: 0.0510 seconds in total
fitting terminal residue with 5000 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_Apr__1_12:16:08_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:08_2019_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: (44.8780,12.9550,8.7610) 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"
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 91 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 91 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: (44.8780,12.9550,8.7610) 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)
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_Apr__1_12:16:08_2019_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 92 read successfully
DEBUG:: there were 0 types with no dictionary
0//-32767 {HOH}/ O altLoc :: segid :: pos: (41.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule (and new chain)
1/C/2 {HOH}/ O altLoc :: segid :: pos: (43.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/C/3 {HOH}/ O altLoc :: segid :: pos: (45.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/C/4 {HOH}/ O altLoc :: segid :: pos: (47.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/C/5 {HOH}/ O altLoc :: segid :: pos: (49.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/16 {HOH}/ O altLoc :: segid :: pos: (51.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/17 {HOH}/ O altLoc :: segid :: pos: (53.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/18 {HOH}/ O altLoc :: segid :: pos: (55.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/19 {HOH}/ O altLoc :: segid :: pos: (57.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/20 {HOH}/ O altLoc :: segid :: pos: (59.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/21 {HOH}/ O altLoc :: segid :: pos: (61.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/22 {HOH}/ O altLoc :: segid :: pos: (63.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/23 {HOH}/ O altLoc :: segid :: pos: (65.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/24 {HOH}/ O altLoc :: segid :: pos: (67.5953,8.6865,12.9093) B-factor: 45.0000 added to molecule
1/D/25 {HOH}/ O altLoc :: segid :: pos: (69.5953,8.6865,12.9093) B-factor: 45.0000 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 93 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 94 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 95 read successfully
DEBUG:: there were 1 types with no dictionary
------- resulting_merge_info has size 2
-------- resulting_merge_info[0] {residue-spec-not-set}
-X,-X+Y,-Z+1/3 ->
-1 0 0
-1 1 0
0 0 -1
translations: 0.0000 0.0000 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: (62.5724,-20.4973,95.4680) B-factor: 45.2600
First atom of 506 in second selection 1/B/193 {SER}/ N altLoc :: segid :: pos: (64.4244,-37.8536,121.3880) 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)
| 0.8045, 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: (62.5724,-20.4973,95.4680) B-factor: 45.2600
First atom of 535 in second selection 1/C/190 {GLN}/ N altLoc :: segid :: pos: (-18.2586,-63.0428,111.4250) 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)
| -0.5596, -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: (62.5724,-20.4973,95.4680) B-factor: 45.2600
First atom of 497 in second selection 1/D/193 {SER}/ N altLoc :: segid :: pos: (-0.2911,-72.4822,94.4690) 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)
| -0.4782, -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"
------- resulting_merge_info has size 6
-------- resulting_merge_info[0] {residue-spec-not-set}
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 97 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_0.pdb.gz
------- resulting_merge_info has size 1
-------- resulting_merge_info[0] {residue-spec-not-set}
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_1.pdb.gz
------- resulting_merge_info has size 1
-------- resulting_merge_info[0] {residue-spec-not-set}
INFO:: Matching/moving molecule number 100 to 99
INFO:: LSQ matched 4 atoms
INFO:: 4 matched atoms had:
mean devi: 0.0353
rms devi: 0.0378
max devi: 0.0545
min devi: 0.0167
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_Apr__1_12:16:10_2019_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
::::: (74 "A" 1 "") #f #f
::::: (74 "A" 4 "") #t #t
::::: (74 "A" 57 "") #t #t
::::: (74 "A" 60 "") #f #f
::::: (74 "A" 61 "") #f #f
::::: (74 "A" 92 "") #t #t
::::: (74 "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 101 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 102 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 101 to 102
INFO:: LSQ matched 164 atoms
INFO:: 164 matched atoms had:
mean devi: 0.5023
rms devi: 0.5938
max devi: 1.6785
min devi: 0.0432
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_Apr__1_12:16:10_2019_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 103 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_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 104 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 105 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 106 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
INFO:: 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:: 0.0010 seconds for contour map
INFO:: 0.0520 seconds in total
masking....masking done
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:10_2019_modification_0.pdb.gz
INFO:: replace_coords: 745 atoms updated.
SFAC LINE: SFAC C H N O S
INFO:: CELL set to 5.9028 13.6977 9.2374 90.0000 98.2110 90.0000
READ-INS:: Spacegroup: "P 1 21/c 1"
INFO:: read_file() chain with chain id has 2 residues
Symmetry available for this molecule
Molecule 108 read successfully
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O CO
INFO:: CELL set to 34.3243 34.3243 11.0887 90.0000 90.0000 90.0000
READ-INS:: Spacegroup: "I 41 2 2"
INFO:: read_file() chain with chain id has 2 residues
Symmetry available for this molecule
Molecule 109 read successfully
INFO:: spacegroup: I 41 2 2
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O S
INFO:: CELL set to 77.7260 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 110 read successfully
Map statistics: mean: -0.0001 st.d: 0.3052
Map statistics: min: -0.7810, max: 6.0791
-0.6953 231
-0.5238 4724
-0.3523 24910
-0.1808 55291
-0.0093 95241
0.1622 40930
0.3337 7480
0.5052 3968
0.6767 2790
0.8482 2117
1.0197 1738
1.1912 1221
1.3628 888
1.5343 595
1.7058 355
1.8773 240
2.0488 137
2.2203 97
2.3918 62
2.5633 46
2.7348 17
2.9063 17
3.0778 13
3.2493 10
3.4208 7
3.5923 1
3.7638 3
3.9353 7
4.1068 2
4.2783 5
4.4498 1
4.6213 2
4.7928 2
4.9643 0
5.1358 1
5.3073 0
5.4788 0
5.6503 0
5.8218 0
5.9933 1
6.1648 0
Map statistics: mean: -0.0000 st.d: 0.0468
Map statistics: min: -0.2115, max: 0.6486
-0.2008 7
-0.1793 48
-0.1578 209
-0.1363 787
-0.1148 2257
-0.0933 5676
-0.0717 12730
-0.0502 24380
-0.0287 38190
-0.0072 46230
0.0143 43880
0.0358 32484
0.0573 19420
0.0788 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 ((104 "A" 1 "") (104 "A" 2 "") (104 "A" 3 "") (104 "A" 4 "") (104 "A" 5 "") (104 "A" 6 "") (104 "A" 7 "") (104 "A" 8 "") (104 "A" 9 "") (104 "A" 10 "") (104 "A" 11 "") (104 "A" 12 "") (104 "A" 13 "") (104 "A" 14 "") (104 "A" 15 "") (104 "A" 16 "") (104 "A" 17 "") (104 "A" 18 "") (104 "A" 19 "") (104 "A" 20 "") (104 "A" 21 "") (104 "A" 22 "") (104 "A" 23 "") (104 "A" 24 "") (104 "A" 25 "") (104 "A" 26 "") (104 "A" 27 "") (104 "A" 28 "") (104 "A" 29 "") (104 "A" 30 "") (104 "A" 31 "") (104 "A" 32 "") (104 "A" 33 "") (104 "A" 34 "") (104 "A" 35 "") (104 "A" 36 "") (104 "A" 37 "") (104 "A" 38 "") (104 "A" 39 "") (104 "A" 40 "") (104 "A" 41 "") (104 "A" 42 "") (104 "A" 43 "") (104 "A" 44 "") (104 "A" 45 "") (104 "A" 46 "") (104 "A" 47 "") (104 "A" 48 "") (104 "A" 49 "") (104 "A" 50 "") (104 "A" 51 "") (104 "A" 52 "") (104 "A" 53 "") (104 "A" 54 "") (104 "A" 55 "") (104 "A" 56 "") (104 "A" 57 "") (104 "A" 58 "") (104 "A" 59 "") (104 "A" 60 "") (104 "A" 61 "") (104 "A" 62 "") (104 "A" 63 "") (104 "A" 64 "") (104 "A" 65 "") (104 "A" 66 "") (104 "A" 67 "") (104 "A" 68 "") (104 "A" 69 "") (104 "A" 70 "") (104 "A" 71 "") (104 "A" 72 "") (104 "A" 73 "") (104 "A" 74 "") (104 "A" 75 "") (104 "A" 76 "") (104 "A" 77 "") (104 "A" 78 "") (104 "A" 79 "") (104 "A" 80 "") (104 "A" 81 "") (104 "A" 82 "") (104 "A" 83 "") (104 "A" 84 "") (104 "A" 85 "") (104 "A" 86 "") (104 "A" 87 "") (104 "A" 88 "") (104 "A" 89 "") (104 "A" 90 "") (104 "A" 91 "") (104 "A" 92 "") (104 "A" 93 "") (104 "B" 1 "") (104 "B" 2 "") (104 "B" 3 "") (104 "B" 4 "") (104 "B" 5 "") (104 "B" 6 "") (104 "B" 7 "") (104 "B" 8 "") (104 "B" 9 "") (104 "B" 10 "") (104 "B" 11 "") (104 "B" 12 "") (104 "B" 13 "") (104 "B" 14 "") (104 "B" 15 "") (104 "B" 16 "") (104 "B" 17 "") (104 "B" 18 "") (104 "B" 19 "") (104 "B" 20 "") (104 "B" 21 "") (104 "B" 22 "") (104 "B" 23 "") (104 "B" 24 "") (104 "B" 25 "") (104 "B" 26 "") (104 "B" 27 "") (104 "B" 28 "") (104 "B" 29 "") (104 "B" 30 "") (104 "B" 31 "") (104 "B" 32 "") (104 "B" 33 "") (104 "B" 34 "") (104 "B" 35 "") (104 "B" 36 "") (104 "B" 37 "") (104 "B" 38 "") (104 "B" 39 "") (104 "B" 40 "") (104 "B" 41 "") (104 "B" 42 "") (104 "B" 43 "") (104 "B" 44 "") (104 "B" 45 "") (104 "B" 46 "") (104 "B" 47 "") (104 "B" 48 "") (104 "B" 49 "") (104 "B" 50 "") (104 "B" 51 "") (104 "B" 52 "") (104 "B" 53 "") (104 "B" 54 "") (104 "B" 55 "") (104 "B" 56 "") (104 "B" 57 "") (104 "B" 58 "") (104 "B" 59 "") (104 "B" 60 "") (104 "B" 61 "") (104 "B" 62 "") (104 "B" 63 "") (104 "B" 64 "") (104 "B" 65 "") (104 "B" 66 "") (104 "B" 67 "") (104 "B" 68 "") (104 "B" 69 "") (104 "B" 70 "") (104 "B" 71 "") (104 "B" 72 "") (104 "B" 73 "") (104 "B" 74 "") (104 "B" 75 "") (104 "B" 76 "") (104 "B" 77 "") (104 "B" 78 "") (104 "B" 79 "") (104 "B" 80 "") (104 "B" 81 "") (104 "B" 82 "") (104 "B" 83 "") (104 "B" 84 "") (104 "B" 85 "") (104 "B" 86 "") (104 "B" 87 "") (104 "B" 88 "") (104 "B" 89 "") (104 "B" 90 "") (104 "B" 91 "") (104 "B" 92 "") (104 "B" 93 "") (104 "B" 94 "") (104 "B" 95 "") (104 "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 testcafitting terminal residue with 5000 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_Apr__1_12:16:13_2019_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/atom_selection_from_insulin.res_Mon_Apr__1_12:16:13_2019_modification_1.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_Apr__1_12:16:13_2019_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: (3.0000,-1.0000,60.0000) B-factor: 45.0000 added to molecule
INFO:: Protein centre at: xyz = ( -0.2998, 10.6, 57.56)
using sigma cut off 0.6000
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.3052
INFO:: Using density cut-off: 0.1831 (0.6000 sigma) (mean -0.0203 stdev: 0.1119)
INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4000 3.2000
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_Apr__1_12:16:13_2019_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 42.1400 83.0300 89.7900 90.0000 90.0000 90.0000
READ-INS:: Spacegroup: "P 21 21 21"
INFO:: read_file() chain with chain id has 5 residues
Symmetry available for this molecule
Molecule 115 read successfully
LATT LINE: LATT -1
SFAC LINE: SFAC C H N O MG CL
INFO:: CELL set to 14.0800 32.7600 18.6600 90.0000 101.7300 90.0000
READ-INS:: Spacegroup: "P 1 21 1"
INFO:: read_file() chain with chain id has 23 residues
Symmetry available for this molecule
Molecule 116 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 14.0800 32.7600 18.6600 90.0000 101.7300 90.0000
READ-INS:: Spacegroup: "P 1 21 1"
INFO:: read_file() chain with chain id A has 23 residues
Symmetry available for this molecule
Molecule 117 read successfully
LATT LINE: LATT -2
SFAC LINE: SFAC S
INFO:: CELL set to 108.9990 108.9990 107.5550 90.0000 90.0000 90.0000
READ-INS:: Spacegroup: "I 4 2 2"
INFO:: read_file() chain with chain id has 4 residues
Symmetry available for this molecule
Molecule 118 read successfully
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/3GP_from_dict_Mon_Apr__1_12:16:13_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/3GP_from_dict_Mon_Apr__1_12:16:13_2019_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 120 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:16:13_2019_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.
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 121 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.
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 122 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: comp-id: LIG is marked for non-autoloading - stopping now
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 123 read successfully
DEBUG:: there were 0 types with no dictionary
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/3GP_from_dict_Mon_Apr__1_12:16:16_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:16:16_2019_modification_0.pdb.gz
------- resulting_merge_info has size 1
-------- resulting_merge_info[0] [spec: mmdb::MinInt4 "L" 1 ""]
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 125 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:16:16_2019_modification_0.pdb.gz
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
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 126 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 132 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
INFO:: Number of observed reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 187.4540 seconds to read MTZ file
INFO:: 7.1540 seconds to initialize map
INFO:: 0.0800 seconds for FFT
INFO:: 0.0120 seconds for statistics
Map mean: ........ -0.0000
Map sigma: ....... 0.1712
Map maximum: ..... 1.3430
Map minimum: ..... -0.6954
INFO:: 0.0010 seconds for contour map
INFO:: 194.7010 seconds in total
INFO:: making difference map from MTZ filename /home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
INFO:: Number of observed reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.0880 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0780 seconds for FFT
INFO:: 0.0110 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.0334
Map maximum: ..... 0.3661
Map minimum: ..... -0.1917
INFO:: 0.0010 seconds for contour map
INFO:: 0.1790 seconds in total
INFO:: ligand number 0 is molecule number 126 with wiggly flag: 0
in execute_ligand_search_internal() import maps from mol 133
INFO:: Protein centre at: xyz = ( 58.29, 34.65, 30.63)
Map statistics: mean: -0.0217 st.d: 0.0886
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
-0.0975 58214
-0.0612 102889
-0.0250 142998
0.0113 471776
0.0475 106846
0.0837 56087
0.1200 21597
0.1562 6911
0.1925 2135
0.2287 920
0.2650 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 (1.0000 sigma) (mean -0.0217 stdev: 0.0886)
INFO:: Blobs with volume larger than 11.0000 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4000 3.2000
INFO:: Finding clusters...done
debug:: n_ligands_for_cluster() top_score 4.0420 and 4 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -50.8108
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 40) at -136.5529
Final Estimated RMS Z Scores:
bonds: 0.1074
angles: 0.0375
torsions: N/A
planes: 0.0573
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 408.9230
Refinement elapsed time: 0.0340
INFO:: backup file coot-backup/Fitted_ligand_#0-0_Mon_Apr__1_12:19:33_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.0180 and 8 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 17.1202
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 26) at -73.5591
Final Estimated RMS Z Scores:
bonds: 0.0457
angles: 0.0446
torsions: N/A
planes: 0.0429
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 409.8660
Refinement elapsed time: 0.0940
INFO:: backup file coot-backup/Fitted_ligand_#1-0_Mon_Apr__1_12:19:34_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.0901 and 4 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 12.8997
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 38) at -66.2704
Final Estimated RMS Z Scores:
bonds: 0.0572
angles: 0.0249
torsions: N/A
planes: 0.0223
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 410.3220
Refinement elapsed time: 0.0150
INFO:: backup file coot-backup/Fitted_ligand_#2-0_Mon_Apr__1_12:19:34_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.8588 and 6 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 34.4825
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 34) at -50.5138
Final Estimated RMS Z Scores:
bonds: 0.0557
angles: 0.0295
torsions: N/A
planes: 0.0472
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 410.9840
Refinement elapsed time: 0.0210
INFO:: backup file coot-backup/Fitted_ligand_#3-0_Mon_Apr__1_12:19:35_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.3913 and 10 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 51.8558
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 27) at -59.5303
Final Estimated RMS Z Scores:
bonds: 0.0792
angles: 0.0310
torsions: N/A
planes: 0.0932
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 412.1190
Refinement elapsed time: 0.0650
INFO:: backup file coot-backup/Fitted_ligand_#4-0_Mon_Apr__1_12:19:36_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.6844 and 8 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: -0.4462
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 48) at -117.4501
Final Estimated RMS Z Scores:
bonds: 0.0872
angles: 0.0841
torsions: N/A
planes: 0.1411
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 413.0340
Refinement elapsed time: 0.0630
INFO:: backup file coot-backup/Fitted_ligand_#5-0_Mon_Apr__1_12:19:37_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.0961 and 8 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 10.7928
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 35) at -74.4890
Final Estimated RMS Z Scores:
bonds: 0.0457
angles: 0.0362
torsions: N/A
planes: 0.0895
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 413.9170
Refinement elapsed time: 0.0220
INFO:: backup file coot-backup/Fitted_ligand_#6-0_Mon_Apr__1_12:19:38_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.6363 and 8 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 29.7970
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 20) at -60.2968
Final Estimated RMS Z Scores:
bonds: 0.0520
angles: 0.0428
torsions: N/A
planes: 0.1954
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 414.8240
Refinement elapsed time: 0.0550
INFO:: backup file coot-backup/Fitted_ligand_#7-0_Mon_Apr__1_12:19:39_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 2.0701 and 3 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 13.4723
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 60) at -92.2098
Final Estimated RMS Z Scores:
bonds: 0.1330
angles: 0.1400
torsions: N/A
planes: 0.0669
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 415.2760
Refinement elapsed time: 0.1150
INFO:: backup file coot-backup/Fitted_ligand_#8-0_Mon_Apr__1_12:19:39_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
debug:: n_ligands_for_cluster() top_score 1.8574 and 5 are decent out of 12
INFO:: created 39 restraints
created 15 bond restraints
created 22 angle restraints
created 2 plane restraints
created 0 chiral vol restraints
Link restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
Flanking residue restraints:
0 bond links
0 angle links
0 plane links
0 trans-peptide links
0 parallel plane restraints
INFO:: make_restraints(): made 58 non-bonded restraints
calling update_refinement_atoms()
initial distortion_score: 21.5046
Initial RMS Z values
bonds: 2.3219
angles: 0.0256
torsions: N/A
planes: 0.0260
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
Minimum found (iteration number 41) at -65.4430
Final Estimated RMS Z Scores:
bonds: 0.0309
angles: 0.0108
torsions: N/A
planes: 0.0708
non-bonded: 0.0000
chiral vol: N/A
rama plot: N/A
start_pos: N/A
GemanMcCl: N/A
SUCCESS
TIME:: (dragged refinement): 415.8510
Refinement elapsed time: 0.0280
INFO:: backup file coot-backup/Fitted_ligand_#9-0_Mon_Apr__1_12:19:40_2019_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
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 146 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of__home_paule_data_greg-data_monomer-3GP.pdb_Mon_Apr__1_12:19:40_2019_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
dirty mmCIF file? /home/paule/data/greg-data/libcheck_3GP.cif
Bad mmdb::mmcif::CIFRC_Ok on ReadMMCIFFile
Unknown error.
CIF error rc=-13 reason:can't open CIF file
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 148 read successfully
DEBUG:: there were 0 types with no dictionary
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 148
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 148
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 149 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
INFO:: 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:: 0.0190 seconds for FFT
INFO:: 0.0030 seconds for statistics
Map mean: ........ 0.0000
Map sigma: ....... 0.3115
Map maximum: ..... 2.9776
Map minimum: ..... -0.8750
INFO:: 0.0010 seconds for contour map
INFO:: 0.0520 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 149
Sequence: ?EYTVITPGARTR
Confidence: 1.0000
From : HEYTVITPGARTR
Chain id: 0 Offset: 53
INFO:: backup file coot-backup/_home_paule_data_greg-data_crashes_on_cootaneering-v2.pdb_Mon_Apr__1_12:19:41_2019_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: 0.0000
rms devi: 0.0000
max devi: 0.0000
min devi: 0.0000
INFO:: 5 matched atoms had:
mean devi: 0.0121
rms devi: 0.0134
max devi: 0.0214
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.2702
rms devi: 0.3350
max devi: 0.5360
min devi: 0.0846
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: 0.3350
max devi: 0.5360
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: 0.0120
rms devi: 0.0133
max devi: 0.0213
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.0002
rms devi: 0.0002
max devi: 0.0003
min devi: 0.0002
INFO:: 5 matched atoms had:
mean devi: 0.2702
rms devi: 0.3350
max devi: 0.5360
min devi: 0.0846
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: 0.0001
rms devi: 0.0001
max devi: 0.0001
min devi: 0.0001
INFO:: 5 matched atoms had:
mean devi: 0.0120
rms devi: 0.0134
max devi: 0.0214
min devi: 0.0039
INFO:: 5 matched atoms had:
mean devi: 0.0001
rms devi: 0.0001
max devi: 0.0001
min devi: 0.0001
INFO:: 5 matched atoms had:
mean devi: 0.0120
rms devi: 0.0134
max devi: 0.0213
min devi: 0.0039
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: 0.0848
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_Apr__1_12:19:41_2019_modification_0.pdb.gz
------- resulting_merge_info has size 2
-------- resulting_merge_info[0] {residue-spec-not-set}
INFO:: Matching/moving molecule number 153 to 153
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: 0.0283
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_Apr__1_12:19:42_2019_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 154 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 155 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()
returing from do_Ca_or_P_bonds_internal() with atom_centres size 0
returing from do_Ca_or_P_bonds_internal() with atom_centres size 0
INFO:: reference 154 has 750 atoms selected
INFO:: moving 155 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_Apr__1_12:19:42_2019_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
returing from do_Ca_or_P_bonds_internal() with atom_centres size 0
INFO: core rmsd achieved: 1.0199 Angstroems
number of residues in reference structure: 322
number of residues in moving structure: 324
number of residues in aligned sections (reference): 100
number of residues in aligned sections (moving): 110
number of aligned residues: 95
number of gaps: 4
number of misdirections: 0
number of SSE combinations: 4.0000
sequence identity: 30.5263%
WARNING:: Error reading /home/paule/data/greg-data/1pyd.pdb
se - new molecule by atom selection inherits shelx molecule flag
PASS: new molecule by atom selection inherits shelx molecule flag
Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy
PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy
Entered testcase - Add water to SHELX molecule
PASS: Add water to SHELX molecule
Entered testcase - Find Waters for a SHELXL molecule
PASS: Find Waters for a SHELXL molecule
Entered testcase - NPD Anisotropic Atom [Mitch Miller]
PASS: NPD Anisotropic Atom [Mitch Miller]
Entered testcase - close shelx molecules
PASS: close shelx molecules
Entered testcase - Aniso Bs in P21
b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018)
b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018)
PASS: Aniso Bs in P21
Entered testcase - Don't crash on reading a strange HAT file
PASS: Don't crash on reading a strange HAT file
Ended 02-shelx.scm
Running 03-ligand.scm ...
Entered testcase - Get monomer test
PASS: Get monomer test
Entered testcase - Delete all-molecule Hydrogens
here 1
PASS: Delete all-molecule Hydrogens
Entered testcase - Non-Autoloads
PASS: Non-Autoloads
Entered testcase - Merge molecules of a ligand with a spec
PASS: Merge molecules of a ligand with a spec
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: 4.79714893189444
distance d2: 2.66560074985002e-7
PASS: flip residue (around eigen vectors)
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 149 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf ""
PASS: Cootaneer Beta Strand
Ended 04-cootaneer.scm
Running 05-rna-ghosts.scm ...
Entered testcase - RNA NCS Ghosts
There are 8 residues in chain "A"
There are 8 residues in chain "B"
PASS: RNA NCS Ghosts
Ended 05-rna-ghosts.scm
Running 06-ssm.scm ...
Entered testcase - SSM - Frank von Delft's Example
PASS: SSM - Frank von Delft's Example
Entered testcase - SSM - Alice Dawson's Example
0 "/home/paule/data/greg-data/tutorial-modern.pdb"
2 "/home/paule/data/greg-data/ins-code-fragment-pre.pdb"
3 "/home/paule/data/greg-data/tutorial-modern.pdb"
4 "PTR_from_dict"
5 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
6 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
7 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
8 "test-3hfl.map"
9 "/home/paule/data/greg-data/tutorial-modern.pdb"
10 "mainchain-forward"
11 "/home/paule/data/greg-data/tutorial-modern.pdb"
12 "mainchain-forwards"
13 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb"
14 "atom selection from tutorial-add-terminal-1-test.pdb"
15 "/home/paule/data/greg-data/frag-2wot.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 "sphere selection from tutorial-modern.pdb"
20 "/home/paule/data/greg-data/rotamer-test-fragment.pdb"
21 "/home/paule/data/greg-data/res098.pdb"
22 "/home/paule/data/greg-data/tutorial-modern.pdb"
23 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
24 "/home/paule/data/greg-data/pdb3knw.ent"
25 "/home/paule/data/greg-data/pdb1py3.ent"
28 "/home/paule/data/greg-data/alt-conf-pepflip-test.pdb"
29 "/home/paule/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb"
32 "/home/paule/data/greg-data/tutorial-modern.pdb"
33 "atom selection from tutorial-modern.pdb"
34 "/home/paule/data/greg-data/tutorial-modern.pdb"
35 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
36 "/home/paule/data/greg-data/tutorial-add-terminal-1-test.pdb"
37 "/home/paule/data/greg-data/tutorial-modern.pdb"
38 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
39 "/home/paule/data/greg-data/tutorial-modern.pdb"
40 "/home/paule/data/greg-data/alt-conf-waters.pdb"
41 "/home/paule/data/greg-data/backrub-fragment.pdb"
42 "Copy_of_/home/paule/data/greg-data/backrub-fragment.pdb"
43 "/home/paule/data/greg-data/coords-B3A.pdb"
44 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT"
45 "/home/paule/data/greg-data/test-TER-OXT.pdb"
46 "/home/paule/data/greg-data/val.pdb"
47 "/home/paule/data/greg-data/2yie-frag.pdb"
48 "/home/paule/data/greg-data/4f8g.pdb"
49 "/home/paule/data/greg-data/4f8g.pdb"
50 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
51 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
52 "/home/paule/data/greg-data/tutorial-modern.pdb"
53 "Generic Masked Map"
54 "difference-map"
57 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
58 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
59 "averaged-map"
60 "difference-map"
61 "/home/paule/data/greg-data/multi-carbo-coot-3.pdb"
62 "/home/paule/data/greg-data/pdb2qc1-sans-cho.pdb"
63 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
64 "/home/paule/data/greg-data/monomer-VAL.pdb"
65 "/home/paule/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb"
66 "atom selection from tutorial-modern.pdb"
67 "/home/paule/data/greg-data/monomer-ACT.pdb"
68 "/home/paule/data/greg-data/tutorial-modern.pdb"
69 "/home/paule/data/greg-data/tutorial-modern.pdb"
70 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
71 "atom selection from tutorial-modern.pdb"
72 "/home/paule/data/greg-data/tutorial-modern.pdb"
73 "/home/paule/data/greg-data/tutorial-modern.pdb"
74 "/home/paule/data/greg-data/rnase-A-needs-an-insertion.pdb"
75 "/home/paule/data/greg-data/tutorial-modern.pdb"
76 "/home/paule/data/greg-data/tutorial-modern.pdb"
77 "/home/paule/data/greg-data/pdb3hfl.ent"
78 "/home/paule/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
79 "Ideal-A-form-RNA"
80 "Ideal-A-form-RNA"
81 "Ideal-A-form-DNA"
82 "Ideal-A-form-DNA"
83 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
84 "/home/paule/data/greg-data/some-waters-with-ter.pdb"
85 "/home/paule/data/greg-data/tm+some-waters.pdb"
86 "/home/paule/data/greg-data/tutorial-modern.pdb"
87 "/home/paule/data/greg-data/water-test-no-cell.pdb"
88 "/home/paule/data/greg-data/pathological-water-test.pdb"
89 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
90 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
91 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
92 "/home/paule/data/greg-data/tutorial-modern.pdb"
93 "/home/paule/data/greg-data/pdb1hvv.ent"
94 "/home/paule/data/greg-data/monomer-ACT.pdb"
95 "/home/paule/data/greg-data/monomer-NPO.pdb"
96 "SymOp_-X,-X+Y,-Z+1/3_Copy_of_93"
97 "/home/paule/data/greg-data/tutorial-modern.pdb"
98 "atom selection from tutorial-modern.pdb"
99 "Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
100 returing from do_Ca_or_P_bonds_internal() with atom_centres size 0
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 156 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 157 read successfully
DEBUG:: there were 1 types with no dictionary
INFO:: reference 156 has 169 atoms selected
INFO:: moving 157 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_Apr__1_12:19:43_2019_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 158 read successfully
INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 108, 132, 64)
INFO:: 0.0280 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:: 0.0010 seconds for contour map
INFO:: 0.0510 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 5 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 159 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 164 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_tutorial-modern.pdb_Mon_Apr__1_12:19:44_2019_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: 164 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 164 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_Apr__1_12:19:44_2019_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_Apr__1_12:19:44_2019_modification_4.pdb.gz
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 164 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 164 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_Apr__1_12:19:44_2019_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 165 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_Apr__1_12:19:44_2019_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: 165 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 165 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_Apr__1_12:19:44_2019_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_paule_data_greg-data_pdb1t6q.ent_Mon_Apr__1_12:19:44_2019_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 166 read successfully
DEBUG:: there were 0 types with no dictionary
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 166 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 167 to 166
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_Apr__1_12:19:44_2019_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 168 to 166
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_Apr__1_12:19:44_2019_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 169 to 166
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_Apr__1_12:19:44_2019_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix:
| -0.2227, -0.9733, -0.05471|
| -0.9662, 0.2129, 0.1454|
| -0.1299, 0.08525, -0.9879|
( -15.82, -0.3228, -130)
INFO:: fractional coordinates matrix:
| -0.7806, -0.3462, 0.03831|
| -1.116, 0.7707, 0.2198|
| -0.09924, 0.106, -0.9879|
( -0.1813, -0.00422, -1.125)
INFO:: Reading coordinate file: /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 170 read successfully
DEBUG:: there were 0 types with no dictionary
INFO:: making map from mtz filename /home/paule/data/greg-data/1hvv_sigmaa.mtz
INFO:: Number of observed reflections: 20903
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO:: grid sampling...Nuvw = ( 112, 112, 150)
INFO:: 11.3040 seconds to read MTZ file
INFO:: 0.0220 seconds to initialize map
INFO:: 0.0330 seconds for FFT
INFO:: 0.0040 seconds for statistics
Map mean: ........ -0.0000
Map sigma: ....... 0.2241
Map maximum: ..... 1.7219
Map minimum: ..... -0.8818
INFO:: 0.0000 seconds for contour map
INFO:: 11.3630 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 171 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 171 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 171 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 171 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 171 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 171 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 171 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 171 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 171 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
"Copy_of_/home/paule/data/greg-data/tutorial-modern.pdb"
101 "/home/paule/data/greg-data/tutorial-modern.pdb"
102 "/home/paule/data/greg-data/pdb1py3.ent"
103 "/home/paule/data/greg-data/tutorial-modern.pdb"
104 "/home/paule/data/greg-data/tutorial-modern.pdb"
105 "/home/paule/data/greg-data/2goz-manip.pdb"
106 "/home/paule/data/greg-data/tutorial-modern.pdb"
107 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
108 "/home/paule/data/greg-data/HOF.RES"
109 "/home/paule/data/greg-data/hollander.ins"
112 "/home/paule/data/greg-data/insulin.fcf Diff-SigmaA"
113 "atom selection from insulin.res"
114 "atom selection from insulin.res"
116 "/home/paule/data/greg-data/horma-p21.res"
117 "new-horma.ins"
118 "/home/paule/data/greg-data/crash.hat"
119 "3GP_from_dict"
120 "/home/paule/data/greg-data/monomer-3GP.pdb"
121 "/home/paule/data/greg-data/test-LIG.pdb"
122 "/home/paule/data/greg-data/test-LIG.pdb"
123 "/home/paule/data/greg-data/tutorial-modern.pdb"
124 "3GP_from_dict"
125 "/home/paule/data/greg-data/monomer-3GP.pdb"
126 "/home/paule/data/greg-data/monomer-NPO.pdb"
127 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
128 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
129 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
130 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
131 "Copy_of_/home/paule/data/greg-data/monomer-NPO.pdb"
132 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb"
133 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT"
134 "/home/paule/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT"
135 "Masked (by protein)"
136 "Fitted ligand #0-0"
137 "Fitted ligand #1-0"
138 "Fitted ligand #2-0"
139 "Fitted ligand #3-0"
140 "Fitted ligand #4-0"
141 "Fitted ligand #5-0"
142 "Fitted ligand #6-0"
143 "Fitted ligand #7-0"
144 "Fitted ligand #8-0"
145 "Fitted ligand #9-0"
146 "/home/paule/data/greg-data/monomer-3GP.pdb"
147 "Copy_of_/home/paule/data/greg-data/monomer-3GP.pdb"
148 "/home/paule/data/greg-data/tutorial-modern.pdb"
149 "/home/paule/data/greg-data/crashes_on_cootaneering-v2.pdb"
150 "/home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
151 "Ideal-A-form-RNA"
154 "/home/paule/data/greg-data/1wly.pdb"
155 "/home/paule/data/greg-data/1yb5.pdb"
PASS: SSM - Alice Dawson's Example
Entered testcase - SSM by atom selection [JED Example]
PASS: SSM by atom selection [JED Example]
Ended 06-ssm.scm
Running 07-ncs.scm ...
Entered testcase - NCS maps test
PASS: NCS maps test
Entered testcase - NCS chains info
NCS info: (("A" "B"))
PASS: NCS chains info
Entered testcase - NCS deviation info
PASS: NCS deviation info
Entered testcase - NCS Residue Range copy
PASS: NCS Residue Range copy
Entered testcase - NCS Residue Range edit to all chains
result: (#t #t)
PASS: NCS Residue Range edit to all chains
Entered testcase - Manual NCS ghosts generates correct NCS chain ids
NCS ghost chain IDs pre: (("B" "A" "C" "D"))
NCS ghost chain IDs post: (("B" "A" "C" "D"))
PASS: Manual NCS ghosts generates correct NCS chain ids
Entered testcase - NCS maps overwrite existing maps
==== test-name: "Map 171 NCS found from matching Chain B onto Chain A" n-matchers: 2
==== test-name: "Map 171 NCS found from matching Chain C onto Chain A" n-matchers: 2
==== test-name: "Map 171 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
PAINFO:: 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 180 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 0.0060 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
SS: 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 130
# of expected passes 128
# of expected failures 0
# of unexpected passes 0
# of unexpected failures 1
# of unresolved testcases 1
# 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 130
# of expected passes 128
# of expected failures 0
# of unexpected passes 0
# of unexpected failures 1
# of unresolved testcases 1
# of unsupported testcases 0
# of untested testcases 0
# of files abandoned 0
ObjectCache: Leaked 0005 refs to <P 2ac 2ab Nuvw = ( 108, 132, 64)>
ObjectCache: Leaked 0004 refs to <C 2c 2 Nuvw = ( 160, 160, 336)>
ObjectCache: Leaked 0005 refs to <P 2ac 2ab>
ObjectCache: Leaked 0004 refs to <C 2c 2>
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well. For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
(coot-crash-catcher.scm:5163): Gtk-WARNING **: cannot open display:
test_coot: coot test failed