testing with greg
testing with greg
currently we are here:
/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre
Thu  2 Jan 17:08:09 GMT 2020
WARNING:: ccp4 setup file setup-ccp4 does not exist.
/d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/
INFO:: Reading coordinate file: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/standard-residues.pdb
 PDB file /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
initalize graphics molecules...done.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)

** (process:24008): WARNING **: 17:08:10.314: Widget is NULL: menubar1
WARNING:: remove_file_curlew_menu_item_maybe() ooops no menubar
(use-graphics-interface-state)
INFO:: coot.py imported
Running python script /d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Afternoon Paul, Welcome to Coot version 0.8.9.3-pre
(set-display-intro-string "Good Afternoon Paul, Welcome to Coot version 0.8.9.3-pre")
(use-graphics-interface-state)
Running python script /home/emsley/.coot-preferences/add_terminal_residue_working.py
Running python script /home/emsley/.coot-preferences/contact_dots.py
Running python script /home/emsley/.coot-preferences/coot_probe_dots.py
Running python script /home/emsley/.coot-preferences/dragged_refinement.py
Running python script /home/emsley/.coot-preferences/long_residues_refine.py
Running python script /home/emsley/.coot-preferences/rama_plot.py
Running python script /home/emsley/.coot-preferences/rotamer.py
Running python script /home/emsley/.coot-preferences/startup.py
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(set-display-intro-string "Good afternoon Paul. Welcome to Coot 0.8.9.3-pre")
(set-display-lists-for-maps 0)
load /home/emsley/.coot-preferences/coot-preferences.scm
(set-filter-fileselection-filenames 1)
(set-sticky-sort-by-date)
(set-colour-map-rotation-on-read-pdb 21.00)
(set-colour-map-rotation-on-read-pdb-c-only-flag 1)
(set-density-size 18.00)
(set-swap-difference-map-colours 0)
(set-colour-map-rotation-for-map 14.00)
(set-active-map-drag-flag 1)
(set-idle-function-rotate-angle  1.00)
load /home/emsley/.coot-preferences/delete-sidechain-key.scm
load /home/emsley/.coot-preferences/delete-sidechain-keybinding.scm
load /home/emsley/.coot-preferences/h-bond-restraints.scm
load /home/emsley/.coot-preferences/morph-residues-gui.scm
load /home/emsley/.coot-preferences/pepflip-complicado.scm
load /home/emsley/.coot-preferences/refine-utils.scm
load /home/emsley/.coot-preferences/restraints.scm
load /home/emsley/.coot-preferences/startup.scm
(set-display-lists-for-maps 0)
load /home/emsley/.coot-preferences/template-key-bindings.scm
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
INFO:: There are 1 command line scripts to run
    command-line-greg.scm
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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/emsley/data/greg-data/2WF6.cif
 mmCIF file /home/emsley/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/emsley/data/greg-data/ins-code-fragment-pre.pdb
 PDB file /home/emsley/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_emsley_data_greg-data_ins-code-fragment-pre.pdb_Thu_Jan__2_17:08:10_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Thu_Jan__2_17:08:10_2020_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Thu_Jan__2_17:08:10_2020_modification_2.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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_Thu_Jan__2_17:08:10_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_modification_1.pdb.gz
INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_modification_2.pdb.gz
INFO:: Matching/moving molecule number 4 to 3
INFO:: LSQ matched 15 atoms
INFO:: 15 matched atoms had: 
   mean devi: 0.577852
    rms devi: 0.627183
    max devi: 0.94351
    min devi: 0.276538
INFO:: Axis orientation: (     0.746,  -0.01099,   -0.6659)
INFO:: Rotation in CCP4 Polar Angles: Polar = (131.748,-0.84427,52.3113)
INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_modification_3.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|    0.8276,    0.5237,   -0.2017|
|   -0.5301,    0.6114,   -0.5875|
|   -0.1843,    0.5932,    0.7837|
(     19.67,     35.56,     6.621)
No unit cell for this molecule, hence no fractional matrix.
INFO:: backup file coot-backup/PTR_from_dict_Thu_Jan__2_17:08:10_2020_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
WARNING:: in torsion match() quad moving not all non-blank
------ after matching, check the torsions 
   torsion check:  ( N    CA   CB   CG )  was   65.41  should be  -47.18 and is  -47.18
   torsion check:  ( CA   CB   CG   CD2)  was   71.13  should be  -56.84 and is  -56.84
   torsion check:  ( O    C    CA   CB )  was  -63.23  should be  -44.77 and is  -44.77
INFO:: rotated 3 torsions in matching torsions
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:10_2020_modification_0.pdb.gz
------- resulting_merge_info has size 1
-------- resulting_merge_info[0] [spec: 1 "A" 101 ""]
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:10_2020_modification_1.pdb.gz
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 86 :: 86 ::  altconf "" coords mol: 3 map mol: -1
INFO:: created 39 restraints

created 16 bond       restraints 
created 22 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: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 706 non-bonded restraints
calling update_refinement_atoms() 
initial distortion_score: 211900.15
    Initial RMS Z values
bonds:      12.79
angles:     9.70
torsions:   N/A 
planes:     12.47
non-bonded: 290.63
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 2) at 118.66
    Final Estimated RMS Z Scores:
bonds:      0.09
angles:     1.94
torsions:   N/A 
planes:     1.03
non-bonded: 0.00
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 0.00
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:10_2020_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/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.60
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.03 seconds to read MTZ file
INFO:: 0.05 seconds to initialize map
INFO:: 0.05 seconds for FFT
INFO:: 0.01 seconds for statistics
      Map mean: ........ 0.00
      Map sigma: ....... 0.31
      Map maximum: ..... 3.12
      Map minimum: ..... -0.91
INFO:: 0.00 seconds for contour map
INFO:: 0.14 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/emsley/data/greg-data/broken.mtz
INFO:: not an mtz file: /home/emsley/data/greg-data/broken.mtz
INFO:: making conventional map from MTZ filename /home/emsley/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 2.60
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.02 seconds to read MTZ file
INFO:: 0.00 seconds to initialize map
INFO:: 0.05 seconds for FFT
INFO:: 0.01 seconds for statistics
      Map mean: ........ 0.00
      Map sigma: ....... 0.31
      Map maximum: ..... 3.12
      Map minimum: ..... -0.91
INFO:: 0.00 seconds for contour map
INFO:: 0.08 seconds in total
INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz
INFO:: Number of observed reflections: 17920
INFO:: finding ASU unique map points with sampling rate 2.60
INFO:: grid sampling...Nuvw = ( 108, 160, 162)
INFO:: 0.02 seconds to read MTZ file
INFO:: 0.03 seconds to initialize map
INFO:: 0.04 seconds for FFT
INFO:: 0.01 seconds for statistics
      Map mean: ........ 0.00
      Map sigma: ....... 0.26
      Map maximum: ..... 1.78
      Map minimum: ..... -1.03
INFO:: 0.00 seconds for contour map
INFO:: 0.10 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: 1.78
     -1.00    7
     -0.93    41
     -0.86    191
     -0.78    586
     -0.71    1746
     -0.64    4206
     -0.57    9248
     -0.50    17586
     -0.43    29941
     -0.36    45756
     -0.29    67360
     -0.22    97280
     -0.15    143881
     -0.08    199949
     -0.01    227160
      0.06    192478
      0.13    118867
      0.20    62666
      0.27    36677
      0.34    27550
      0.41    23779
      0.48    20707
      0.55    18091
      0.62    15228
      0.69    12099
      0.76    9240
      0.83    6657
      0.90    4375
      0.97    2822
      1.05    1624
      1.12    867
      1.19    461
      1.26    237
      1.33    130
      1.40    83
      1.47    49
      1.54    23
      1.61    18
      1.68    9
      1.75    5
      1.82    0
INFO:: n grid points:             1399680
INFO:: mean before filtering:     0.00
INFO:: variance before filtering: 0.07
INFO:: filter by ignoring 995 of 1399680 counts ( = 0.0711%) with values around 0.0065 from bin 3685 of 10000
      Map mean: ........ -0.0000
      Map rmsd: ........ 0.2605
      Map maximum: ..... 1.7844
      Map minimum: ..... -1.0312
WARNING:: Error reading .
. is a directory.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 
/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures successfully opened
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
68 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
136 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
56 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
9 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
23 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
172 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
494 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
142 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
33 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
123 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
174 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
51 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
205 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
318 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
72 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
24 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
520 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
119 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
364 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
64 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
140 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
20 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
35 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
294 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
14 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
54 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
218 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
208 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
75 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
349 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
52 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
13 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
145 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
106 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
326 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
171 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
45 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
68 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
137 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
411 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
108 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
4 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
131 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
129 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
143 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
155 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
127 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb
There was an error reading /d/emsley/autobuild/install-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: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
226 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
247 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
108 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
543 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
149 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
29 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
228 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
     Adding fragments from: /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
0 fragments garnered from /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/reference-structures/1i40.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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:12_2020_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:24008): Gtk-CRITICAL **: 17:08:13.057: IA__gtk_widget_show: assertion 'GTK_IS_WIDGET (widget)' failed
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb
 PDB file /home/emsley/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_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:13_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:13_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb
 PDB file /home/emsley/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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0330 seconds to read MTZ file
INFO:: 0.0020 seconds to initialize map
INFO:: 0.0560 seconds for FFT
INFO:: 0.0080 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.1010 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
------------------ add_view_raw() B11 View
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:13_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:13_2020_modification_1.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:13_2020_modification_2.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/rotamer-test-fragment.pdb
 PDB file /home/emsley/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 ""]
INFO:: Reading coordinate file: /home/emsley/data/greg-data/eleanor-HIS.pdb
 PDB file /home/emsley/data/greg-data/eleanor-HIS.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 21 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/res098.pdb
 PDB file /home/emsley/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 22 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG:: In copy_mol_and_refine() refine range: chain  :X: 15 :: 15 ::  altconf "" coords mol: 22 map mol: -1
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 128 non-bonded restraints
calling update_refinement_atoms() 
initial distortion_score: 2951.2431
    Initial RMS Z values
bonds:      0.8732
angles:     1.0078
torsions:   N/A 
planes:     0.5766
non-bonded: 22.6696
chiral vol: 0.3851
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 10) at 1603.0629
    Final Estimated RMS Z Scores:
bonds:      4.5730
angles:     3.3091
torsions:   N/A 
planes:     1.8776
non-bonded: 8.9511
chiral vol: 0.7470
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 2.9090
debug:: restraints results 1 5 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_res098.pdb_Thu_Jan__2_17:08:14_2020_modification_0.pdb.gz
INFO:: replace_coords: 11 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 23 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0440 seconds to read MTZ file
INFO:: 0.0040 seconds to initialize map
INFO:: 0.0690 seconds for FFT
INFO:: 0.0100 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.1290 seconds in total
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:15_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:15_2020_modification_1.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 12.1008
Good afternoon Paul Emsley. Welcome to Coot 0.8.9.3-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: 1.33847240473201
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 0.311500996351242 #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
dd-1: 0.0 dd-2: 2.36045066887977
PASS: 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-fit rotamINFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3knw.ent
 PDB file /home/emsley/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 25 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3knw.ent_Thu_Jan__2_17:08:15_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent
 PDB file /home/emsley/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 26 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_emsley_data_greg-data_pdb1py3.ent_Thu_Jan__2_17:08:15_2020_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
er 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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 27 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0280 seconds to read MTZ file
INFO:: 0.0020 seconds to initialize map
INFO:: 0.0510 seconds for FFT
INFO:: 0.0080 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.0910 seconds in total
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:15_2020_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/emsley/data/greg-data/alt-conf-pepflip-test.pdb
 PDB file /home/emsley/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 29 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-pepflip-test.pdb_Thu_Jan__2_17:08:15_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb
 PDB file /home/emsley/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 30 read successfully
DEBUG:: there were 0 types with no dictionary 
------------------ add_view_raw() CIS-TRANS cispep View
omega: 1 12.7704 degrees 
INFO This is a CIS peptide - making it TRANS
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_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_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_2.pdb.gz
DEBUG:: ================ refine_residue_range: 30 A 11:: 12:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 11 :: 12 ::  altconf "" coords mol: 30 map mol: 5
debug:: in refine_residues_vec() with altconf ""
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 137 non-bonded restraints
calling update_refinement_atoms() 
initial distortion_score: 6702.4094
    Initial RMS Z values
bonds:      14.8983
angles:     8.7656
torsions:   N/A 
planes:     3.4883
non-bonded: 41.0829
chiral vol: 3.2117
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -3111.9438
    Final Estimated RMS Z Scores:
bonds:      3.7624
angles:     2.2634
torsions:   N/A 
planes:     2.5430
non-bonded: 10.2967
chiral vol: 0.7311
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 4.1620
Refinement elapsed time: 0.1780
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_3.pdb.gz
INFO:: replace_coords: 11 atoms updated.
INFO:: mutate 11 A to a LEU
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_5.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 8.7591
DEBUG:: ================ refine_residue_range: 30 A 11:: 12:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 11 :: 12 ::  altconf "" coords mol: 30 map mol: 5
debug:: in refine_residues_vec() with altconf ""
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 221 non-bonded restraints
calling update_refinement_atoms() 
initial distortion_score: -4219.2183
    Initial RMS Z values
bonds:      3.5118
angles:     2.4494
torsions:   N/A 
planes:     2.7241
non-bonded: 6.8639
chiral vol: 0.8372
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 2) at -4391.6571
    Final Estimated RMS Z Scores:
bonds:      3.2832
angles:     2.0277
torsions:   N/A 
planes:     2.6195
non-bonded: 6.3741
chiral vol: 0.5811
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 4.3580
Refinement elapsed time: 0.1150
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Jan__2_17:08:15_2020_modification_6.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 31 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:16_2020_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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 33 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:08:16_2020_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_Thu_Jan__2_17:08:16_2020_modification_1.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 35 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0240 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0470 seconds for FFT
INFO:: 0.0080 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.0820 seconds in total
DEBUG:: ================ refine_residue_range: 35 B 72:: 72:: :B: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :B: 72 :: 72 ::  altconf "B" coords mol: 35 map mol: 36
debug:: in refine_residues_vec() with altconf "B"
INFO:: created 10 restraints

created 5 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 64 non-bonded restraints
calling update_refinement_atoms() 
initial distortion_score: -2362.5539
    Initial RMS Z values
bonds:      2.9785
angles:     1.3074
torsions:   N/A 
planes:     0.6113
non-bonded: 0.8668
chiral vol: 0.8558
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -2507.9378
    Final Estimated RMS Z Scores:
bonds:      0.7572
angles:     0.8546
torsions:   N/A 
planes:     0.4816
non-bonded: 0.0779
chiral vol: 0.5526
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 4.7430
Refinement elapsed time: 0.1530
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:16_2020_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb
 PDB file /home/emsley/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 37 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:16_2020_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0 
debug:: split_residue() returned 0 ""
debug:: in refine_residues_vec() with altconf ""
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: -15850.1474
    Initial RMS Z values
bonds:      2.6203
angles:     1.5627
torsions:   N/A 
planes:     0.8383
non-bonded: 0.0007
chiral vol: 0.6412
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 2) at -16343.7575
    Final Estimated RMS Z Scores:
bonds:      1.0276
angles:     0.7800
torsions:   N/A 
planes:     0.6346
non-bonded: 0.0000
chiral vol: 0.1566
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 5.1210
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:16_2020_modification_1.pdb.gz
INFO:: replace_coords: 39 atoms updated.
debug:: in refine_residues_vec() with altconf ""
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: -7240.6588
    Initial RMS Z values
bonds:      2.1848
angles:     1.4708
torsions:   N/A 
planes:     1.7875
non-bonded: 5.2955
chiral vol: 10.5313
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -15861.6327
    Final Estimated RMS Z Scores:
bonds:      1.5657
angles:     2.0166
torsions:   N/A 
planes:     1.9124
non-bonded: 0.0735
chiral vol: 1.2451
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.7640
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Jan__2_17:08:16_2020_modification_2.pdb.gz
INFO:: replace_coords: 41 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 38 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0240 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0460 seconds for FFT
INFO:: 0.0080 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.0810 seconds in total
DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 40 :: 43 ::  altconf "" coords mol: 38 map mol: 39
debug:: in refine_residues_vec() with altconf ""
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: -3045.0595
    Initial RMS Z values
bonds:      2.0802
angles:     1.5577
torsions:   N/A 
planes:     1.9846
non-bonded: 7.4770
chiral vol: 11.7704
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -11482.4822
    Final Estimated RMS Z Scores:
bonds:      1.6070
angles:     2.2751
torsions:   N/A 
planes:     2.0946
non-bonded: 0.0963
chiral vol: 1.4573
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 8.2150
Refinement elapsed time: 1.3190
DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 40 :: 43 ::  altconf "" coords mol: 38 map mol: 39
debug:: in refine_residues_vec() with altconf ""
----------------------------------------------
----------------------------------------------
     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: 4736.2655
    Initial RMS Z values
bonds:      2.0802
angles:     1.5577
torsions:   N/A 
planes:     1.9846
non-bonded: 7.4770
chiral vol: 11.7704
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -3096.1965
    Final Estimated RMS Z Scores:
bonds:      0.6605
angles:     1.6575
torsions:   N/A 
planes:     2.2513
non-bonded: 0.0350
chiral vol: 0.7040
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 10.6730
Refinement elapsed time: 2.4580
DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 40 :: 43 ::  altconf "" coords mol: 38 map mol: 39
debug:: in refine_residues_vec() with altconf ""
----------------------------------------------
----------------------------------------------
     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: 6082.7324
    Initial RMS Z values
bonds:      2.0802
angles:     1.5577
torsions:   N/A 
planes:     1.9846
non-bonded: 7.4770
chiral vol: 11.7704
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -1687.9568
    Final Estimated RMS Z Scores:
bonds:      0.4814
angles:     1.4444
torsions:   N/A 
planes:     2.1530
non-bonded: 0.0218
chiral vol: 0.5373
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 21.9080
Refinement elapsed time: 11.2340
DEBUG:: ================ refine_residue_range: 38 A 40:: 43:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 40 :: 43 ::  altconf "" coords mol: 38 map mol: 39
debug:: in refine_residues_vec() with altconf ""
----------------------------------------------
----------------------------------------------
     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: 6537.2933
    Initial RMS Z values
bonds:      2.0802
angles:     1.5577
torsions:   N/A 
planes:     1.9846
non-bonded: 7.4770
chiral vol: 11.7704
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -1179.0725
    Final Estimated RMS Z Scores:
bonds:      0.3794
angles:     1.2107
torsions:   N/A 
planes:     1.9961
non-bonded: 0.0103
chiral vol: 0.5195
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 23.5970
Refinement elapsed time: 1.6890
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 40 read successfully
DEBUG:: there were 0 types with no dictionary 
debug:: in refine_residues_vec() with altconf ""
----------------------------------------------
----------------------------------------------
     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: -1608.3783
    Initial RMS Z values
bonds:      2.6094
angles:     1.4906
torsions:   N/A 
planes:     0.7374
non-bonded: 0.0256
chiral vol: 0.8303
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -1917.2396
    Final Estimated RMS Z Scores:
bonds:      0.1670
angles:     0.7090
torsions:   N/A 
planes:     0.4424
non-bonded: 0.0032
chiral vol: 0.3186
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 24.1340
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:35_2020_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=0.279831287906342
PASS: Refine Zone with Alt conf
Entered testcase - Sphere Refine
======= got bond length 1.31073682992
PASS: Sphere Refine
Entered testcase - Refinement gives useful results
   refinement results: ("" 0 (("Bonds" "Bonds:    1.607" 1.6069860458374) ("Angles" "Angles:   2.275" 2.27508354187012) ("Planes" "Planes:   2.095" 2.09464716911316) ("Non-bonded" "Non-bonded:   0.310" 0.310280948877335) ("Chirals" "Chirals:   1.457" 1.45725882053375)))
   ow factor: 1.85849389433861
   INFO:: setting refinement weight to 17.371166104535
   refinement results: ("" 0 (("Bonds" "Bonds:    0.661" 0.660505056381226) ("Angles" "Angles:   1.658" 1.65754890441895) ("Planes" "Planes:   2.251" 2.25134062767029) ("Non-bonded" "Non-bonded:   0.187" 0.187022611498833) ("Chirals" "Chirals:   0.704" 0.703979432582855)))
   ow factor: 1.31834350526333
   INFO:: setting refinement weight to 9.99474706905847
   refinement results: ("" 0 (("Bonds" "Bonds:    0.481" 0.481422454118729) ("Angles" "Angles:   1.444" 1.44444286823273) ("Planes" "Planes:   2.153" 2.15304064750671) ("Non-bonded" "Non-bonded:   0.148" 0.147786349058151) ("Chirals" "Chirals:   0.537" 0.537297546863556)))
   ow factor: 1.15405087918043
   INFO:: setting refinement weight to 7.50450238272587
   refinement results: ("" 0 (("Bonds" "Bonds:    0.379" 0.379440784454346) ("Angles" "Angles:   1.211" 1.21067309379578) ("Planes" "Planes:   1.996" 1.99607837200165) ("Non-bonded" "Non-bonded:   0.101" 0.101409189403057) ("Chirals" "Chirals:   0.520" 0.519510805606842)))
   ow factor: 1.02642576396465
PASS: Refinement gives useful results
Entered testcase - Neighbour-Refine doesn't destroy disulfide bonds
bond-length-within-tolerance? bond-length 2.03197508776284 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6101188659668 27.522180557251 11.2309684753418)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.7754211425781 27.0276489257812 9.44557189941406))
debug:: in refine_residues_vec() with altconf ""
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: -1917.2396
    Initial RMS Z values
bonds:      0.1670
angles:     0.7090
torsions:   N/A 
planes:     0.4424
non-bonded: 0.0032
chiral vol: 0.3186
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -1917.2423
    Final Estimated RMS Z Scores:
bonds:      0.1674
angles:     0.7089
torsions:   N/A 
planes:     0.4426
non-bonded: 0.0032
chiral vol: 0.3183
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 24.1840
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:08:35_2020_modification_1.pdb.gz
INFO:: replace_coords: 27 atoms updated.
bond-length-within-tolerance? bond-length 2.03197644083519 with target 2.0 and tolerance 0.05 for atom ((" SG " "") (1.0 17.4099998474121 " S" "") (25.6100997924805 27.5221691131592 11.2309703826904)) is ((" SG " "") (1.0 17.4899997711182 " S" "") (24.775426864624 27.0276279449463 9.44556331634521))
INFO:: Reading coordinate file: /home/emsley/data/greg-data/alt-conf-waters.pdb
 PDB file /home/emsley/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 41 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG:: ================ refine_residue_range: 41 D 71:: 71:: :A: 1
masking....masking done
INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-waters.pdb_Thu_Jan__2_17:08:35_2020_modification_0.pdb.gz
INFO:: replace_coords: 1 atoms updated.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
INFO:: Reading coordinate file: /home/emsley/data/greg-data/backrub-fragment.pdb
 PDB file /home/emsley/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 42 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Thu_Jan__2_17:08:35_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Thu_Jan__2_17:08:35_2020_modification_1.pdb.gz
INFO:: replace_coords: 14 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/coords-B3A.pdb
 PDB file /home/emsley/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 44 read successfully
DEBUG:: there were 1 types with no dictionary 
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 44 map mol: -1
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 7) at 0.0001
    Final Estimated RMS Z Scores:
bonds:      0.0011
angles:     0.0034
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0000
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 24.4750
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Thu_Jan__2_17:08:36_2020_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/lib-B3A.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/lib-B3A.cif had no bond restraints
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 44 map mol: -1
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: 0.0001
    Initial RMS Z values
bonds:      0.0011
angles:     0.0034
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0000
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:      0.0014
angles:     0.0027
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0003
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 24.6050
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Thu_Jan__2_17:08:36_2020_modification_1.pdb.gz
INFO:: replace_coords: 6 atoms updated.
Welcome to Coot
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 44 map mol: -1
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: 3.0104
    Initial RMS Z values
bonds:      0.6699
angles:     0.3748
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.2531
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at 0.0001
    Final Estimated RMS Z Scores:
bonds:      0.0012
angles:     0.0041
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0010
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 24.7180
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Thu_Jan__2_17:08:36_2020_modification_2.pdb.gz
INFO:: replace_coords: 6 atoms updated.
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0250 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0470 seconds for FFT
INFO:: 0.0070 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.0820 seconds in total
INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-TER-OXT.pdb
 PDB file /home/emsley/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 46 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_test-TER-OXT.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/val.pdb
 PDB file /home/emsley/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 47 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: mutate 3 C to a HIS
INFO:: backup file coot-backup/_home_emsley_data_greg-data_val.pdb_Thu_Jan__2_17:08:36_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/2yie-frag.pdb
 PDB file /home/emsley/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 48 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_2yie-frag.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/4f8g.pdb
 PDB file /home/emsley/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 1 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/4f8g.pdb
 PDB file /home/emsley/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 50 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Thu_Jan__2_17:08:36_2020_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/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0240 seconds to read MTZ file
INFO:: 0.0020 seconds to initialize map
INFO:: 0.0470 seconds for FFT
INFO:: 0.0080 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.0830 seconds in total
INFO:: making map from mtz filename /home/emsley/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:: 0.0230 seconds to read MTZ file
INFO:: 0.0290 seconds to initialize map
INFO:: 0.0300 seconds for FFT
INFO:: 0.0050 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:: 0.0880 seconds in total
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 53 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: -0.9116, max: 3.1176
   -0.8613    21
   -0.7605    144
   -0.6598    1355
   -0.5591    8283
   -0.4583    34328
   -0.3576    88827
   -0.2569    140726
   -0.1562    185091
   -0.0554    222101
    0.0453    222174
    0.1460    111281
    0.2468    50680
    0.3475    29724
    0.4482    22854
    0.5490    19216
    0.6497    16308
    0.7504    13864
    0.8512    11002
    0.9519    8557
    1.0526    6028
    1.1534    4257
    1.2541    2950
    1.3548    1917
    1.4555    1136
    1.5563    670
    1.6570    352
    1.7577    210
    1.8585    91
    1.9592    24
    2.0599    14
    2.1607    7
    2.2614    8
    2.3621    7
    2.4629    8
    2.5636    2
    2.6643    2
    2.7650    3
    2.8658    0
    2.9665    1
    3.0672    0
    3.1680    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: (0.992907404899597 0.960582137107849 0.99147617816925 0.666360557079315 0.677083969116211 0.822775840759277 0.746499538421631 1.12646055221558 1.03679931163788 1.02070951461792 0.81580126285553)  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: 0.0602
Map statistics: min: -3.0391, max: 0.7582
   -2.9917    2
   -2.8967    1
   -2.8018    2
   -2.7069    2
   -2.6119    4
   -2.5170    5
   -2.4221    3
   -2.3271    4
   -2.2322    9
   -2.1373    5
   -2.0423    3
   -1.9474    11
   -1.8525    7
   -1.7575    10
   -1.6626    27
   -1.5677    17
   -1.4727    51
   -1.3778    80
   -1.2829    105
   -1.1879    157
   -1.0930    184
   -0.9981    302
   -0.9031    394
   -0.8082    517
   -0.7133    579
   -0.6184    639
   -0.5234    839
   -0.4285    934
   -0.3336    1114
   -0.2386    1318
   -0.1437    1755
   -0.0488    339081
    0.0462    845092
    0.1411    3721
    0.2360    3127
    0.3310    2324
    0.4259    1272
    0.5208    410
    0.6158    95
    0.7107    21
    0.8056    1
   diff-high-values: (0.00614375341683626 0.00179204856976867 0.00554320681840181 0.00859612133353949 0.00364016066305339 0.00399892218410969 0.00163731398060918 0.00837583001703024 0.00694983452558517 0.00368036120198667 0.0069606532342732)  diff-low-values: (-0.908486723899841 -0.95145583152771 -1.25011610984802 -1.226642370224 -1.11153709888458 -0.85110729932785 -0.853124260902405 -0.707162618637085 -0.954133033752441 -0.566797137260437)
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 56 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0240 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0460 seconds for FFT
INFO:: 0.0080 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0020 seconds for contour map
INFO:: 0.0800 seconds in total
INFO:: making map from mtz filename /home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
INFO:: Number of observed reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.6000
INFO:: grid sampling...Nuvw = ( 192, 224, 112)
INFO:: 0.0240 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0450 seconds for FFT
INFO:: 0.0080 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 3.1176
      Map minimum: ..... -0.9116
INFO:: 0.0010 seconds for contour map
INFO:: 0.0790 seconds in total
INFO:: making map from mtz filename /home/emsley/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:: 0.0240 seconds to read MTZ file
INFO:: 0.0410 seconds to initialize map
INFO:: 0.0420 seconds for FFT
INFO:: 0.0060 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:: 0.1150 seconds in total
INFO:: multiplying map (function index) 0 Nuvw = ( 192, 224, 112) 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: -0.9080, max: 3.1098
   -0.8578    23
   -0.7573    157
   -0.6569    1462
   -0.5564    8793
   -0.4560    36076
   -0.3555    91860
   -0.2551    144385
   -0.1547    189058
   -0.0542    225530
    0.0462    197979
    0.1467    112236
    0.2471    51757
    0.3476    30773
    0.4480    23747
    0.5484    20007
    0.6489    16994
    0.7493    14466
    0.8498    11446
    0.9502    8941
    1.0507    6285
    1.1511    4436
    1.2516    3081
    1.3520    2004
    1.4524    1203
    1.5529    697
    1.6533    376
    1.7538    224
    1.8542    97
    1.9547    38
    2.0551    16
    2.1555    13
    2.2560    17
    2.3564    13
    2.4569    11
    2.5573    6
    2.6578    6
    2.7582    4
    2.8587    3
    2.9591    2
    3.0595    1
    3.1600    1
Map statistics: mean: 0.0000 st.d: 0.0011
Map statistics: min: -0.0111, max: 0.0150
   -0.0108    1
   -0.0101    1
   -0.0095    3
   -0.0088    1
   -0.0082    2
   -0.0075    9
   -0.0068    27
   -0.0062    93
   -0.0055    244
   -0.0049    747
   -0.0042    1999
   -0.0036    4699
   -0.0029    10741
   -0.0023    24133
   -0.0016    56083
   -0.0010    150373
   -0.0003    369547
    0.0003    357690
    0.0010    134126
    0.0016    47222
    0.0023    21496
    0.0029    11213
    0.0036    6131
    0.0043    3424
    0.0049    1958
    0.0056    1091
    0.0062    557
    0.0069    329
    0.0075    154
    0.0082    60
    0.0088    30
    0.0095    15
    0.0101    5
    0.0108    7
    0.0114    2
    0.0121    4
    0.0127    3
    0.0134    2
    0.0141    0
    0.0147    2
    0.0154    0
INFO:: Reading coordinate file: /home/emsley/data/greg-data/multi-carbo-coot-3.pdb
 PDB file /home/emsley/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 62 read successfully
DEBUG:: there were 2 types with no dictionary 
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 2 ::  altconf "" coords mol: 62 map mol: -1
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): 27.0880
debug:: restraints results 1 5 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_multi-carbo-coot-3.pdb_Thu_Jan__2_17:08:38_2020_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 0.311070144176483 and diff-map: 0.00108510116115212
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/emsley/data/greg-data/pdb2qc1-sans-cho.pdb
 PDB file /home/emsley/data/greg-data/pdb2qc1-sans-cho.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 3 links
in add_molecular_symmetry_matrices() made 1 biomt matrices
INFO:: NCS chain comparison 4/110
Molecule 63 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/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:: 0.0230 seconds to read MTZ file
INFO:: 0.0100 seconds to initialize map
INFO:: 0.0150 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
......... checking for /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab
..that failed - trying  /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/NAG-decorations.tab
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_1.pdb.gz
INFO:: link torsion generated from link bond restraint
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_2.pdb.gz
INFO:: replace_coords: 22 atoms updated.
debug:: in refine_residues_vec() with altconf ""
INFO:: created 55 restraints

created 21 bond       restraints 
created 27 angle      restraints 
created 2 plane      restraints 
created 5 chiral vol restraints 
Link restraints: 
   1 bond    links
   3 angle   links
   1 plane   links
   0 trans-peptide links
   0 parallel plane restraints
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 697 non-bonded restraints
calling update_refinement_atoms() 
initial distortion_score: 61627.5852
    Initial RMS Z values
bonds:      1.0337
angles:     3.2356
torsions:   N/A 
planes:     6.9590
non-bonded: 87.9889
chiral vol: 0.3636
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_3.pdb.gz
INFO:: replace_coords: 22 atoms updated.
debug:: in refine_residues_vec() with altconf ""
INFO:: created 55 restraints

created 21 bond       restraints 
created 27 angle      restraints 
created 2 plane      restraints 
created 5 chiral vol restraints 
Link restraints: 
   1 bond    links
   3 angle   links
   1 plane   links
   0 trans-peptide links
   0 parallel plane restraints
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 451 non-bonded restraints
calling update_refinement_atoms() 
initial distortion_score: 19857.6554
    Initial RMS Z values
bonds:      0.4642
angles:     1.0934
torsions:   N/A 
planes:     0.7818
non-bonded: 44.8200
chiral vol: 0.4827
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 1) at -489.0507
    Final Estimated RMS Z Scores:
bonds:      0.4320
angles:     0.9119
torsions:   N/A 
planes:     0.8150
non-bonded: 0.0022
chiral vol: 0.5075
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 49.1210
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb2qc1-sans-cho.pdb_Thu_Jan__2_17:08:38_2020_modification_4.pdb.gz
INFO:: replace_coords: 22 atoms updated.
PASS: Make a glycosidic linkage
Entered testcase - Refine an NAG-ASN Link
bond-length-within-tolerance? bond-length 1.43597463820273 with target 1.43 and tolerance 0.2 for atom ((" ND2" "") (1.0 16.9300003051758 " N" "") (-15.001612663269 -0.467886626720428 -7.01484489440918)) is ((" C1 " "") (1.0 45.0 " C" "") (-14.0559310913086 -0.695992231369019 -5.95858860015869))
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-VAL.pdb
 PDB file /home/emsley/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 65 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: found bad VAL chiral atom: A 1   CB  
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 65 map mol: -1
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: 21.7281
    Initial RMS Z values
bonds:      0.7365
angles:     0.7519
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0277
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 3) at 0.0153
    Final Estimated RMS Z Scores:
bonds:      0.0019
angles:     0.0238
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0322
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 49.2230
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: undo molecule number set to: 65
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_1.pdb.gz
restoring from backup 2 2
INFO:: Reading coordinate file: coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_0.pdb.gz
 PDB file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_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
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 65 map mol: -1
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: 21.7281
    Initial RMS Z values
bonds:      0.7365
angles:     0.7519
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0277
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 3) at 0.0153
    Final Estimated RMS Z Scores:
bonds:      0.0019
angles:     0.0238
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0322
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 49.3250
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Thu_Jan__2_17:09:00_2020_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
PASS: Refine an NAG-ASN Link
Entered testcase - Test for flying hydrogens on undo
bond-length-within-tolerance? bond-length 0.972985777356827 with target 0.96 and tolerance 0.02 for atom (("HG11" "") (1.0 20.0 " H" "") (3.48122096061707 -0.187875345349312 -1.98467183113098)) is ((" CG1" "") (1.0 20.0 " C" "") (2.8759868144989 -0.203856721520424 -1.2230042219162))
INFO:: Reading coordinate file: /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb
 PDB file /home/emsley/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 66 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG:: In copy_mol_and_refine() refine range: chain  :B: 6 :: 6 ::  altconf "" coords mol: 66 map mol: -1
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: 2263.3054
    Initial RMS Z values
bonds:      7.1303
angles:     6.7178
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0334
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 5) at 0.0469
    Final Estimated RMS Z Scores:
bonds:      0.0022
angles:     0.0379
torsions:   N/A 
planes:     N/A 
non-bonded: 0.0000
chiral vol: 0.0489
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 49.4310
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Thu_Jan__2_17:09:01_2020_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 0.973010154757159 with target 0.96 and tolerance 0.02 for atom (("HD11" "") (1.0 10.5299997329712 " H" "") (-10.1254034042358 6.53209161758423 7.00641536712646)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1308145523071 5.64076614379883 6.61621236801147))
bond-length-within-tolerance? bond-length 0.972997348417048 with target 0.96 and tolerance 0.02 for atom (("HD12" "") (1.0 10.1300001144409 " H" "") (-9.76907539367676 5.68026351928711 5.71382188796997)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1308145523071 5.64076614379883 6.61621236801147))
bond-length-within-tolerance? bond-length 0.972972386005099 with target 0.96 and tolerance 0.02 for atom (("HD13" "") (1.0 10.5600004196167 " H" "") (-11.0441112518311 5.30675506591797 6.58457374572754)) is ((" CD1" "") (1.0 11.5200004577637 " C" "") (-10.1308145523071 5.64076614379883 6.61621236801147))
bond-length-within-tolerance? bond-length 0.972992004194165 with target 0.96 and tolerance 0.02 for atom (("HD21" "") (1.0 10.1499996185303 " H" "") (-7.98362302780151 3.13911032676697 7.13967418670654)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55780792236328 3.69762277603149 6.58732557296753))
bond-length-within-tolerance? bond-length 0.973016117814419 with target 0.96 and tolerance 0.02 for atom (("HD22" "") (1.0 10.3000001907349 " H" "") (-9.21132946014404 3.13903474807739 6.13163995742798)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55780792236328 3.69762277603149 6.58732557296753))
bond-length-within-tolerance? bond-length 0.97300876474718 with target 0.96 and tolerance 0.02 for atom (("HD23" "") (1.0 10.6499996185303 " H" "") (-8.01666164398193 4.16603326797485 5.92816066741943)) is ((" CD2" "") (1.0 11.960000038147 " C" "") (-8.55780792236328 3.69762277603149 6.58732557296753))
DEBUG:: ================ refine_residue_range: 67 A 30:: 30:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 30 :: 30 ::  altconf "" coords mol: 67 map mol: 5
debug:: in refine_residues_vec() with altconf ""
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: 2760.1885
    Initial RMS Z values
bonds:      2.7809
angles:     1.0747
torsions:   N/A 
planes:     3.0558
non-bonded: 79.8585
chiral vol: 1.1767
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 2) at -492.4876
    Final Estimated RMS Z Scores:
bonds:      0.2639
angles:     0.2999
torsions:   N/A 
planes:     0.3241
non-bonded: 0.0214
chiral vol: 0.0559
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 49.8850
Refinement elapsed time: 0.3910
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:09:01_2020_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: 2.62147952908895: 
bond-length-within-tolerance? bond-length 2.62147952908895 with target 2.8 and tolerance 0.6 for atom ((" CB " "") (1.0 21.75 " C" "") (67.3067474365234 4.49700593948364 19.8036155700684)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.5366897583008 6.70065450668335 19.0941581726074))
DEBUG:: ================ refine_residue_range: 67 A 30:: 30:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 30 :: 30 ::  altconf "" coords mol: 67 map mol: 5
debug:: in refine_residues_vec() with altconf ""
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: 11905.0124
    Initial RMS Z values
bonds:      32.1444
angles:     0.2999
torsions:   N/A 
planes:     0.3241
non-bonded: 0.0000
chiral vol: 0.0559
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 2) at -544.8533
    Final Estimated RMS Z Scores:
bonds:      0.0765
angles:     0.1076
torsions:   N/A 
planes:     0.3525
non-bonded: 0.0000
chiral vol: 0.0750
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 50.1290
Refinement elapsed time: 0.2250
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:09:01_2020_modification_1.pdb.gz
INFO:: replace_coords: 12 atoms updated.
   pass intermediate 2.8 tolerance test
  OK plane atom " CB "
   Bond-length: 1.50860713059272: 
bond-length-within-tolerance? bond-length 1.50860713059272 with target 1.512 and tolerance 0.04 for atom ((" CB " "") (1.0 21.75 " C" "") (67.5384674072266 4.9270167350769 19.3901653289795)) is ((" CG " "") (1.0 21.9699993133545 " C" "") (68.2881469726563 6.20275497436523 19.0962810516357))
INFO:: wrote mmCIF "coot-test-ala.cif"
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb
 PDB file /home/emsley/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 68 read successfully
DEBUG:: there were 1 types with no dictionary 
Welcome to Coot
WARNING:: bond_restraint_length 4 should be 5
DEBUG:: ================ refine_residue_range: 68 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 68 map mol: 5
debug:: in refine_residues_vec() with altconf ""
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: 4838.0256
    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 
Refinement elapsed time: 0.9380
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-ACT.pdb_Thu_Jan__2_17:09:02_2020_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_1.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 26 A 27 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_2.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_3.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_5.pdb.gz
INFO:: Removing CIS peptide from PDB header: B 26 B 27 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_6.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:02_2020_modification_7.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 70 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 
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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 74 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/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb
 PDB file /home/emsley/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 75 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: aligning to mol number 75 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/emsley/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_emsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Thu_Jan__2_17:09:03_2020_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: 202615928 "A" 1 ""] -> ASP
      [spec: 202615928 "A" 2 ""] -> VAL
      [spec: 202615928 "A" 3 ""] -> SER
      [spec: 202615928 "A" 11 ""] -> LEU
      [spec: 202615928 "A" 12 ""] -> PRO
      [spec: 202615928 "A" 13 ""] -> PRO
      [spec: 202615928 "A" 62 ""] -> PRO
      [spec: 202615928 "A" 63 ""] -> GLY
   Deletions:
      [spec: 202615928 "A" 25 ""]
      [spec: 202615928 "A" 34 ""]
   Mutations:
      [spec: 202615928 "A" 24 ""] -> SER
      [spec: 202615928 "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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 77 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb3hfl.ent
 PDB file /home/emsley/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 78 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/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:: 0.0180 seconds to read MTZ file
INFO:: 0.0050 seconds to initialize map
INFO:: 0.0120 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:: 0.0000 seconds for contour map
INFO:: 0.0370 seconds in total
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Fitting score for best rotamer: 5.8340
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:03_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Thu_Jan__2_17:09:03_2020_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_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/some-waters-with-ter.pdb
 PDB file /home/emsley/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 85 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_some-waters-with-ter.pdb_Thu_Jan__2_17:09:04_2020_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/emsley/data/greg-data/tm+some-waters.pdb
 PDB file /home/emsley/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 86 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 -0.0338 stdev: 0.1463)
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 = (     59.88,     2.985,     -4.28) is too big to be water
INFO:: cluster at xyz = (     70.02,     19.06,     18.65) is too big to be water
INFO:: cluster at xyz = (     53.05,     9.039,     20.15) is too big to be water
INFO:: found 61 waters in water fitting
Done - back from lig.water_fit()
DEBUG::  new_waters_mol_flag: 0
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tm+some-waters.pdb_Thu_Jan__2_17:09:04_2020_modification_0.pdb.gz
INFO:: Adding to solvent chain: D
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 87 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:04_2020_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/emsley/data/greg-data/water-test-no-cell.pdb
 PDB file /home/emsley/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 88 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_water-test-no-cell.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz
No symmetry available
INFO:: moved 0 water molecules
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pathological-water-test.pdb
 PDB file /home/emsley/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 89 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pathological-water-test.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz
INFO:: moved 181 water molecules
INFO:: making map from mtz filename /home/emsley/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:: 0.0230 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0170 seconds for FFT
INFO:: 0.0010 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:: 0.0420 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:07_2020_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: 92 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 92 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:07_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 93 read successfully
DEBUG:: there were 0 types with no dictionary 
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/emsley/data/greg-data/pdb1hvv.ent
 PDB file /home/emsley/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 94 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb
 PDB file /home/emsley/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 95 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb
 PDB file /home/emsley/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 96 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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 98 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_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_Thu_Jan__2_17:09:08_2020_modification_1.pdb.gz
------- resulting_merge_info has size 1
-------- resulting_merge_info[0] {residue-spec-not-set}
INFO:: Matching/moving molecule number 101 to 100
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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_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
    ::::: (75 "A" 1 "") #f #f
    ::::: (75 "A" 4 "") #t #t
    ::::: (75 "A" 57 "") #t #t
    ::::: (75 "A" 60 "") #f #f
    ::::: (75 "A" 61 "") #f #f
    ::::: (75 "A" 92 "") #t #t
    ::::: (75 "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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 102 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent
 PDB file /home/emsley/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 103 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 102 to 103
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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_modification_0.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 105 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/2goz-manip.pdb
 PDB file /home/emsley/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 106 read successfully
DEBUG:: there were 7 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 107 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/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:: 0.0240 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0160 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:: 0.0430 seconds in total
masking....masking done
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:08_2020_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 109 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 110 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 111 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 ((105 "A" 1 "") (105 "A" 2 "") (105 "A" 3 "") (105 "A" 4 "") (105 "A" 5 "") (105 "A" 6 "") (105 "A" 7 "") (105 "A" 8 "") (105 "A" 9 "") (105 "A" 10 "") (105 "A" 11 "") (105 "A" 12 "") (105 "A" 13 "") (105 "A" 14 "") (105 "A" 15 "") (105 "A" 16 "") (105 "A" 17 "") (105 "A" 18 "") (105 "A" 19 "") (105 "A" 20 "") (105 "A" 21 "") (105 "A" 22 "") (105 "A" 23 "") (105 "A" 24 "") (105 "A" 25 "") (105 "A" 26 "") (105 "A" 27 "") (105 "A" 28 "") (105 "A" 29 "") (105 "A" 30 "") (105 "A" 31 "") (105 "A" 32 "") (105 "A" 33 "") (105 "A" 34 "") (105 "A" 35 "") (105 "A" 36 "") (105 "A" 37 "") (105 "A" 38 "") (105 "A" 39 "") (105 "A" 40 "") (105 "A" 41 "") (105 "A" 42 "") (105 "A" 43 "") (105 "A" 44 "") (105 "A" 45 "") (105 "A" 46 "") (105 "A" 47 "") (105 "A" 48 "") (105 "A" 49 "") (105 "A" 50 "") (105 "A" 51 "") (105 "A" 52 "") (105 "A" 53 "") (105 "A" 54 "") (105 "A" 55 "") (105 "A" 56 "") (105 "A" 57 "") (105 "A" 58 "") (105 "A" 59 "") (105 "A" 60 "") (105 "A" 61 "") (105 "A" 62 "") (105 "A" 63 "") (105 "A" 64 "") (105 "A" 65 "") (105 "A" 66 "") (105 "A" 67 "") (105 "A" 68 "") (105 "A" 69 "") (105 "A" 70 "") (105 "A" 71 "") (105 "A" 72 "") (105 "A" 73 "") (105 "A" 74 "") (105 "A" 75 "") (105 "A" 76 "") (105 "A" 77 "") (105 "A" 78 "") (105 "A" 79 "") (105 "A" 80 "") (105 "A" 81 "") (105 "A" 82 "") (105 "A" 83 "") (105 "A" 84 "") (105 "A" 85 "") (105 "A" 86 "") (105 "A" 87 "") (105 "A" 88 "") (105 "A" 89 "") (105 "A" 90 "") (105 "A" 91 "") (105 "A" 92 "") (105 "A" 93 "") (105 "B" 1 "") (105 "B" 2 "") (105 "B" 3 "") (105 "B" 4 "") (105 "B" 5 "") (105 "B" 6 "") (105 "B" 7 "") (105 "B" 8 "") (105 "B" 9 "") (105 "B" 10 "") (105 "B" 11 "") (105 "B" 12 "") (105 "B" 13 "") (105 "B" 14 "") (105 "B" 15 "") (105 "B" 16 "") (105 "B" 17 "") (105 "B" 18 "") (105 "B" 19 "") (105 "B" 20 "") (105 "B" 21 "") (105 "B" 22 "") (105 "B" 23 "") (105 "B" 24 "") (105 "B" 25 "") (105 "B" 26 "") (105 "B" 27 "") (105 "B" 28 "") (105 "B" 29 "") (105 "B" 30 "") (105 "B" 31 "") (105 "B" 32 "") (105 "B" 33 "") (105 "B" 34 "") (105 "B" 35 "") (105 "B" 36 "") (105 "B" 37 "") (105 "B" 38 "") (105 "B" 39 "") (105 "B" 40 "") (105 "B" 41 "") (105 "B" 42 "") (105 "B" 43 "") (105 "B" 44 "") (105 "B" 45 "") (105 "B" 46 "") (105 "B" 47 "") (105 "B" 48 "") (105 "B" 49 "") (105 "B" 50 "") (105 "B" 51 "") (105 "B" 52 "") (105 "B" 53 "") (105 "B" 54 "") (105 "B" 55 "") (105 "B" 56 "") (105 "B" 57 "") (105 "B" 58 "") (105 "B" 59 "") (105 "B" 60 "") (105 "B" 61 "") (105 "B" 62 "") (105 "B" 63 "") (105 "B" 64 "") (105 "B" 65 "") (105 "B" 66 "") (105 "B" 67 "") (105 "B" 68 "") (105 "B" 69 "") (105 "B" 70 "") (105 "B" 71 "") (105 "B" 72 "") (105 "B" 73 "") (105 "B" 74 "") (105 "B" 75 "") (105 "B" 76 "") (105 "B" 77 "") (105 "B" 78 "") (105 "B" 79 "") (105 "B" 80 "") (105 "B" 81 "") (105 "B" 82 "") (105 "B" 83 "") (105 "B" 84 "") (105 "B" 85 "") (105 "B" 86 "") (105 "B" 87 "") (105 "B" 88 "") (105 "B" 89 "") (105 "B" 90 "") (105 "B" 91 "") (105 "B" 92 "") (105 "B" 93 "") (105 "B" 94 "") (105 "B" 95 "") (105 "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_Thu_Jan__2_17:09:10_2020_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_Thu_Jan__2_17:09:10_2020_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_emsley_data_greg-data_insulin.res_Thu_Jan__2_17:09:10_2020_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_emsley_data_greg-data_insulin.res_Thu_Jan__2_17:09:10_2020_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 116 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 117 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 118 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 119 read successfully
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/3GP_from_dict_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/3GP_from_dict_Thu_Jan__2_17:09:10_2020_modification_1.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb
 PDB file /home/emsley/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 121 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb
 PDB file /home/emsley/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:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb
 PDB file /home/emsley/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 123 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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 124 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_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz
------- resulting_merge_info has size 1
-------- resulting_merge_info[0] [spec: mmdb::MinInt4 "L" 1 ""]
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb
 PDB file /home/emsley/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 126 read successfully
DEBUG:: there were 0 types with no dictionary 
------------------ add_view_raw() ligand-view
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:10_2020_modification_0.pdb.gz
DEBUG:: ================ refine_residue_range: 126 A 1:: 1:: :: 0
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb
 PDB file /home/emsley/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 127 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
 PDB file /home/emsley/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 133 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making conventional map from MTZ filename /home/emsley/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:: 0.1230 seconds to read MTZ file
INFO:: 0.0950 seconds to initialize map
INFO:: 0.0710 seconds for FFT
INFO:: 0.0090 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:: 0.2990 seconds in total
INFO:: making difference map from MTZ filename /home/emsley/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:: 0.0730 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0660 seconds for FFT
INFO:: 0.0090 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.0334
      Map maximum: ..... 0.3661
      Map minimum: ..... -0.1917
INFO:: 0.0000 seconds for contour map
INFO:: 0.1490 seconds in total
INFO:: ligand number 0 is molecule number 127   with wiggly flag: 0
in execute_ligand_search_internal() import maps from mol 134
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
DEBUG:: ================ refine_residue_range: 137 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 137 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 137.4962
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.7000
INFO:: backup file coot-backup/Fitted_ligand_#0-0_Thu_Jan__2_17:09:15_2020_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
DEBUG:: ================ refine_residue_range: 138 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 138 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 239.5569
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.7110
INFO:: backup file coot-backup/Fitted_ligand_#1-0_Thu_Jan__2_17:09:18_2020_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
DEBUG:: ================ refine_residue_range: 139 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 139 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 233.2160
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.6780
INFO:: backup file coot-backup/Fitted_ligand_#2-0_Thu_Jan__2_17:09:21_2020_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
DEBUG:: ================ refine_residue_range: 140 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 140 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 265.6423
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.6610
INFO:: backup file coot-backup/Fitted_ligand_#3-0_Thu_Jan__2_17:09:25_2020_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
DEBUG:: ================ refine_residue_range: 141 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 141 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 291.7442
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.7020
INFO:: backup file coot-backup/Fitted_ligand_#4-0_Thu_Jan__2_17:09:28_2020_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
DEBUG:: ================ refine_residue_range: 142 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 142 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 213.1649
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.7290
INFO:: backup file coot-backup/Fitted_ligand_#5-0_Thu_Jan__2_17:09:32_2020_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
DEBUG:: ================ refine_residue_range: 143 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 143 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 230.0505
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.6500
INFO:: backup file coot-backup/Fitted_ligand_#6-0_Thu_Jan__2_17:09:35_2020_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
DEBUG:: ================ refine_residue_range: 144 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 144 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 258.6028
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.6710
INFO:: backup file coot-backup/Fitted_ligand_#7-0_Thu_Jan__2_17:09:39_2020_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
DEBUG:: ================ refine_residue_range: 145 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 145 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 234.0762
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.6720
INFO:: backup file coot-backup/Fitted_ligand_#8-0_Thu_Jan__2_17:09:42_2020_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
DEBUG:: ================ refine_residue_range: 146 A 1:: 1:: :: 0
DEBUG:: In copy_mol_and_refine() refine range: chain  :A: 1 :: 1 ::  altconf "" coords mol: 146 map mol: 134
debug:: in refine_residues_vec() with altconf ""
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: 246.1442
    Initial RMS Z values
bonds:      4.6248
angles:     0.8127
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 
Refinement elapsed time: 2.6680
INFO:: backup file coot-backup/Fitted_ligand_#9-0_Thu_Jan__2_17:09:45_2020_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb
 PDB file /home/emsley/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 147 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_monomer-3GP.pdb_Thu_Jan__2_17:09:45_2020_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
INFO:: Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 149 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 149
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 149
INFO:: Reading coordinate file: /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb
 PDB file /home/emsley/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 150 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/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:: 0.0230 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0160 seconds for FFT
INFO:: 0.0010 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:: 0.0420 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 150

Sequence: ?EYTVITPGARTR
Confidence: 1.0000

From    : HEYTVITPGARTR
Chain id: 0	Offset: 53
INFO:: backup file coot-backup/_home_emsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Thu_Jan__2_17:09:46_2020_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_Thu_Jan__2_17:09:46_2020_modification_0.pdb.gz
------------------ add_view_raw() RNA-builder-view
------- resulting_merge_info has size 2
-------- resulting_merge_info[0] {residue-spec-not-set}
INFO:: Matching/moving molecule number 154 to 154
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_Thu_Jan__2_17:09:46_2020_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.
------------------ add_view_raw() RNA-ghots-view
INFO:: Reading coordinate file: /home/emsley/data/greg-data/1wly.pdb
 PDB file /home/emsley/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 155 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/1yb5.pdb
 PDB file /home/emsley/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 156 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 155 has 750 atoms selected
INFO:: moving    156 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_emsley_data_greg-data_1yb5.pdb_Thu_Jan__2_17:09:47_2020_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%
------------------ add_view_raw() SSM View
WARNING:: Error reading /home/emsley/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 150 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/emsley/data/greg-data/tutorial-modern.pdb"
    2    "/home/emsley/data/greg-data/ins-code-fragment-pre.pdb"
    3    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    4    "PTR_from_dict"
    5    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    6    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    7    "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
    8    "test-3hfl.map"
    9    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    10    "mainchain-forward"
    11    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    12    "mainchain-forwards"
    13    "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb"
    14    "atom selection from tutorial-add-terminal-1-test.pdb"
    15    "/home/emsley/data/greg-data/frag-2wot.pdb"
    16    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    17    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    18    "sphere selection from tutorial-modern.pdb"
    20    "/home/emsley/data/greg-data/rotamer-test-fragment.pdb"
    21    "/home/emsley/data/greg-data/eleanor-HIS.pdb"
    22    "/home/emsley/data/greg-data/res098.pdb"
    23    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    24    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    25    "/home/emsley/data/greg-data/pdb3knw.ent"
    26    "/home/emsley/data/greg-data/pdb1py3.ent"
    29    "/home/emsley/data/greg-data/alt-conf-pepflip-test.pdb"
    30    "/home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb"
    33    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    34    "atom selection from tutorial-modern.pdb"
    35    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    36    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    37    "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb"
    38    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    39    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    40    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    41    "/home/emsley/data/greg-data/alt-conf-waters.pdb"
    42    "/home/emsley/data/greg-data/backrub-fragment.pdb"
    43    "Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb"
    44    "/home/emsley/data/greg-data/coords-B3A.pdb"
    45    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT"
    46    "/home/emsley/data/greg-data/test-TER-OXT.pdb"
    47    "/home/emsley/data/greg-data/val.pdb"
    48    "/home/emsley/data/greg-data/2yie-frag.pdb"
    49    "/home/emsley/data/greg-data/4f8g.pdb"
    50    "/home/emsley/data/greg-data/4f8g.pdb"
    51    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    52    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    53    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    54    "Generic Masked Map"
    55    "difference-map"
    58    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    59    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    60    "averaged-map"
    61    "difference-map"
    62    "/home/emsley/data/greg-data/multi-carbo-coot-3.pdb"
    63    "/home/emsley/data/greg-data/pdb2qc1-sans-cho.pdb"
    64    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    65    "/home/emsley/data/greg-data/monomer-VAL.pdb"
    66    "/home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb"
    67    "atom selection from tutorial-modern.pdb"
    68    "/home/emsley/data/greg-data/monomer-ACT.pdb"
    69    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    70    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    71    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    72    "atom selection from tutorial-modern.pdb"
    73    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    74    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    75    "/home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb"
    76    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    77    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    78    "/home/emsley/data/greg-data/pdb3hfl.ent"
    79    "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
    80    "Ideal-A-form-RNA"
    81    "Ideal-A-form-RNA"
    82    "Ideal-A-form-DNA"
    83    "Ideal-A-form-DNA"
    84    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    85    "/home/emsley/data/greg-data/some-waters-with-ter.pdb"
    86    "/home/emsley/data/greg-data/tm+some-waters.pdb"
    87    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    88    "/home/emsley/data/greg-data/water-test-no-cell.pdb"
    89    "/home/emsley/data/greg-data/pathological-water-test.pdb"
    90    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    91    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    92    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    93    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    94    "/home/emsley/data/greg-data/pdb1hvv.ent"
    95    "/home/emsley/data/greg-data/monomer-ACT.pdb"
    96    "/home/emsley/data/greg-data/monomer-NPO.pdb"
    97    "SymOp_-X,-X+Y,-Z+1/3_Copy_of_94"
    98    "/home/emsley/data/greg-data/tutorial-modern.pdb"
returing from do_Ca_or_P_bonds_internal() with atom_centres size 0
INFO:: Reading coordinate file: /home/emsley/data/greg-data/2qd9.pdb
 PDB file /home/emsley/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 157 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Reading coordinate file: /home/emsley/data/greg-data/2gtn.pdb
 PDB file /home/emsley/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 158 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: reference 157 has 169 atoms selected
INFO:: moving    158 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_emsley_data_greg-data_2gtn.pdb_Thu_Jan__2_17:09:47_2020_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 159 read successfully
INFO:: making map from mtz filename /home/emsley/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:: 0.0240 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0160 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:: 0.0430 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:: 1204224 out of 1204224 (100.0000%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: 0.0003 st.d: 0.3259
Map statistics: min: -1.4625, max: 2.4294
   -1.4139    10
   -1.3166    17
   -1.2193    21
   -1.1220    26
   -1.0247    48
   -0.9274    147
   -0.8301    599
   -0.7328    2202
   -0.6355    7234
   -0.5382    21636
   -0.4409    54191
   -0.3436    104988
   -0.2463    155380
   -0.1490    175625
   -0.0517    165940
    0.0456    135166
    0.1429    101141
    0.2402    76296
    0.3375    58142
    0.4348    43032
    0.5321    31316
    0.6294    22626
    0.7267    15850
    0.8239    11149
    0.9212    7707
    1.0185    5078
    1.1158    3326
    1.2131    2189
    1.3104    1320
    1.4077    786
    1.5050    469
    1.6023    252
    1.6996    123
    1.7969    69
    1.8942    45
    1.9915    31
    2.0888    22
    2.1861    16
    2.2834    5
    2.3807    3
    2.4780    1
INFO:: installing ghost map with name :Map 160 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/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/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 165 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_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: 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 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_3.pdb.gz
INFO:: mutate 2 A to a TRP
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_4.pdb.gz
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 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_emsley_data_greg-data_tutorial-modern.pdb_Thu_Jan__2_17:09:49_2020_modification_5.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1t6q.ent
 PDB file /home/emsley/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 166 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: mutate 50 A to a ASP
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Thu_Jan__2_17:09:49_2020_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: 166 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 166 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_emsley_data_greg-data_pdb1t6q.ent_Thu_Jan__2_17:09:49_2020_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Thu_Jan__2_17:09:49_2020_modification_2.pdb.gz
INFO:: Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent
 PDB file /home/emsley/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 167 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 167 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 168 to 167
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_emsley_data_greg-data_pdb1hvv.ent_Thu_Jan__2_17:09:49_2020_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 169 to 167
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_emsley_data_greg-data_pdb1hvv.ent_Thu_Jan__2_17:09:50_2020_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 170 to 167
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_emsley_data_greg-data_pdb1hvv.ent_Thu_Jan__2_17:09:50_2020_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/emsley/data/greg-data/pdb1hvv.ent
 PDB file /home/emsley/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 171 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making map from mtz filename /home/emsley/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:: 0.0300 seconds to read MTZ file
INFO:: 0.0200 seconds to initialize map
INFO:: 0.0300 seconds for FFT
INFO:: 0.0030 seconds for statistics
      Map mean: ........ -0.0000
      Map sigma: ....... 0.2241
      Map maximum: ..... 1.7219
      Map minimum: ..... -0.8818
INFO:: 0.0000 seconds for contour map
INFO:: 0.0830 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 172 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 172 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 172 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 172 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 172 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 172 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 172 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 172 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 172 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
    99    "atom selection from tutorial-modern.pdb"
    100    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    101    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    102    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    103    "/home/emsley/data/greg-data/pdb1py3.ent"
    104    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    105    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    106    "/home/emsley/data/greg-data/2goz-manip.pdb"
    107    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    108    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    109    "/home/emsley/data/greg-data/HOF.RES"
    110    "/home/emsley/data/greg-data/hollander.ins"
    113    "/home/emsley/data/greg-data/insulin.fcf Diff-SigmaA"
    114    "atom selection from insulin.res"
    115    "atom selection from insulin.res"
    117    "/home/emsley/data/greg-data/horma-p21.res"
    118    "new-horma.ins"
    119    "/home/emsley/data/greg-data/crash.hat"
    120    "3GP_from_dict"
    121    "/home/emsley/data/greg-data/monomer-3GP.pdb"
    122    "/home/emsley/data/greg-data/test-LIG.pdb"
    123    "/home/emsley/data/greg-data/test-LIG.pdb"
    124    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    125    "3GP_from_dict"
    126    "/home/emsley/data/greg-data/monomer-3GP.pdb"
    127    "/home/emsley/data/greg-data/monomer-NPO.pdb"
    128    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    129    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    130    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    131    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    132    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    133    "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb"
    134    "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT"
    135    "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT"
    136    "Masked (by protein)"
    137    "Fitted ligand #0-0"
    138    "Fitted ligand #1-0"
    139    "Fitted ligand #2-0"
    140    "Fitted ligand #3-0"
    141    "Fitted ligand #4-0"
    142    "Fitted ligand #5-0"
    143    "Fitted ligand #6-0"
    144    "Fitted ligand #7-0"
    145    "Fitted ligand #8-0"
    146    "Fitted ligand #9-0"
    147    "/home/emsley/data/greg-data/monomer-3GP.pdb"
    148    "Copy_of_/home/emsley/data/greg-data/monomer-3GP.pdb"
    149    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    150    "/home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb"
    151    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    152    "Ideal-A-form-RNA"
    155    "/home/emsley/data/greg-data/1wly.pdb"
    156    "/home/emsley/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 172 NCS found from matching Chain B onto Chain A"   n-matchers: 2
==== test-name: "Map 172 NCS found from matching Chain C onto Chain A"   n-matchers: 2
==== test-name: "Map 172 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 runerror (syntax error)
error (syntax error)
error (not syntax error)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
NameError: name 'rr_not_found_thing' is not defined
INFO:: Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb
 PDB file /home/emsley/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 181 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/emsley/ccp4/ccp4-7.0/lib/data/monomers/
There are 153 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/A.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/C.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/G.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/u/U.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HOH.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/n/NA.cif
There are 2 data in /home/emsley/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/emsley/ccp4/ccp4-7.0/lib/data/monomers/
There are 153 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/a/A.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/c/C.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/g/G.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/u/U.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/h/HOH.cif
There are 2 data in /home/emsley/ccp4/ccp4-7.0/lib/data/monomers/n/NA.cif
INFO:: Reading coordinate file: /home/emsley/data/greg-data/hideous-OXT.pdb
 PDB file /home/emsley/data/greg-data/hideous-OXT.pdb has been read.
Spacegroup: P 21 21 21
read 9 atom 
created 8 bond       restraints 
created 10 angle      restraints 
created 2 plane      restraints 
created 1 chiral vol restraints 
created 3 torsion restraints 
created 28 restraints

INFO:: make_restraints(): made 13 non-bonded restraints
initial distortion_score: 4671.5846
    Initial RMS Z values
bonds:      5.4612
angles:     16.4829
torsions:   0.3071
planes:     19.5074
non-bonded: 0.0000
chiral vol: 1.0066
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 379) at 7.7980
    Final Estimated RMS Z Scores:
bonds:      0.1934
angles:     0.7875
torsions:   0.0791
planes:     0.0047
non-bonded: 0.0000
chiral vol: 0.0006
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
refinement_took 0.0070 seconds
OXT out of plane distance: 0.0003
OXT->O distance: 2.1787
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/emsley/data/greg-data/frag-2wot.pdb
 PDB file /home/emsley/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
ning a Python function
   test_val_2 passed
   test_val_3 passed
PASS: Test running a Python function
Entered testcase - Internal/External Molecule Numbers match
PASS: Internal/External Molecule Numbers match
Entered testcase - spacegroup operators to space group conversion
PASS: spacegroup operators to space group conversion
Ended 08-utils.scm
Running 09-internal.scm ...
Entered testcase - Test internal functions
PASS: Test internal functions
Ended 09-internal.scm

                === greg-tests Summary ===

# of testcases attempted   130
# of expected passes       130
# of expected failures     0
# of unexpected passes     0
# of unexpected failures   0
# of unresolved testcases  0
# of unsupported testcases 0
# of untested testcases    0

Loading greg-tests/end.grg ...
Loaded greg-tests/end.grg

                === Summary of all tests ===

# of tools                 1
# of testcases attempted   130
# of expected passes       130
# of expected failures     0
# of unexpected passes     0
# of unexpected failures   0
# of unresolved testcases  0
# of unsupported testcases 0
# of untested testcases    0
# of files abandoned       0

ObjectCache: Leaked 0004 refs to <P 2ac 2ab Nuvw = ( 192, 224, 112)>
ObjectCache: Leaked 0004 refs to <C 2c 2 Nuvw = ( 160, 160, 336)>
ObjectCache: Leaked 0004 refs to <P 2ac 2ab>
ObjectCache: Leaked 0004 refs to <C 2c 2>
test_coot: coot test passed