testing with python unittest
testing with python unittest
currently we are here:
/lmb/home/pemsley/autobuild/building/pcterm37.lmb.internal_2016-12-27__T04_00_02/coot-0.8.8-pre
/lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/bin/coot --no-graphics --script python-tests/coot_unittest.py
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/
INFO:: Reading coordinate file: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/standard-residues.pdb
 PDB file /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
initalize graphics molecules...done.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
INFO:: coot.py imported
Running python script /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Paul, Welcome to Coot version 0.8.8-pre
(set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.8.8-pre")
(use-graphics-interface-state)
Running python script /lmb/home/pemsley/.coot-preferences/pepflip-new.py
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(set-display-intro-string "Good morning Paul. Welcome to Coot 0.8.8-pre")
(set-display-lists-for-maps 0)
load /lmb/home/pemsley/.coot-preferences/angle-factor.scm
(set-hardware-stereo-angle-factor  1.50)
load /lmb/home/pemsley/.coot-preferences/coot-preferences.scm
(set-filter-fileselection-filenames 0)
(unset-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 12.60)
(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 /lmb/home/pemsley/.coot-preferences/enhanced-ligand.scm
load /lmb/home/pemsley/.coot-preferences/key-bindings.scm
(set-add-terminal-residue-do-post-refine 1)
(set-terminal-residue-do-rigid-body-refine 0)
load /lmb/home/pemsley/.coot-preferences/template-key-bindings.scm
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
INFO:: There are 1 command line scripts to run
    python-tests/coot_unittest.py
Running python script python-tests/coot_unittest.py
===============================================================
==================== Testing ==================================
===============================================================
WARNING:: unittest skip not avaliable!!!!!!
==== It seems CCP4_MASTER is setup ===
==== CCP4_MASTER: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2
test00_0 (__main__.PdbMtzTestFunctions)
Post Go To Atom no molecule ... INFO:: Command: (post-go-to-atom-window)
ok
test01_0 (__main__.PdbMtzTestFunctions)
Close bad molecule ... INFO:: Command: (close-molecule -2)
ok
test02_0 (__main__.PdbMtzTestFunctions)
Read coordinates test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 0 read successfully
DEBUG:: there were 0 types with no dictionary 
ok
test03_0 (__main__.PdbMtzTestFunctions)
New molecule from bogus molecule ... Molecule number -5 is not a valid model molecule
ok
test03_1 (__main__.PdbMtzTestFunctions)
Don't crash on empty NCS from mmCIF file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2WF6.pdb" 1)
WARNING:: Error reading /lmb/home/pemsley/data/greg-data/2WF6.pdb
   closing molecule number -1
INFO:: Command: (close-molecule -1)
ok
test04_0 (__main__.PdbMtzTestFunctions)
New molecule from bogus atom selection ... in new_molecule_by_atom_selection Something bad happened - No atoms selected
INFO:: Command: (info-dialog "Oops, failed to create fragment.  No atoms selected
Incorrect atom specifier? "//A/100"")
   INFO:: pre_n_molecules 1   post_n_molecules 1
ok
test05_0 (__main__.PdbMtzTestFunctions)
ins code change and Goto atom over an ins code break ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb" 0)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb
 PDB file /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 1 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (set-go-to-atom-molecule 1)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Dec_27_04:13:57_2016_modification_0.pdb.gz
INFO:: Command: (change-residue-number 1 "A" 68 "" 68 "A")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Dec_27_04:13:57_2016_modification_1.pdb.gz
INFO:: Command: (change-residue-number 1 "A" 69 "" 68 "B")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_ins-code-fragment-pre.pdb_Tue_Dec_27_04:13:57_2016_modification_2.pdb.gz
INFO:: Command: (change-residue-number 1 "A" 67 "" 68 "")
   pre and post ins codes:   A
INFO:: Command: (write-pdb-file 1 "post-ins-change.pdb")
   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 ']
ok
test06_0 (__main__.PdbMtzTestFunctions)
Read a bogus map ... WARNING:: Error reading bogus.map
Read map bogus.map failed
ok
test07_0 (__main__.PdbMtzTestFunctions)
Read MTZ test ... WARNING:: Can't find file bogus.mtz
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.058 seconds to read MTZ file
INFO:: 0.032 seconds to initialize map
INFO:: 0.038 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.044 seconds for contour map
INFO:: 0.179 seconds in total
ok
test07_1 (__main__.PdbMtzTestFunctions)
Auto-read bad MTZ test ... WARNING:: file xx-missing.mtz does not exist
CCP4MTZfile: open_read - File missing or corrupted: /lmb/home/pemsley/data/greg-data/broken.mtz
   got status:  ()
>>>>>> CCP4 library signal library_file:End of File (Error)
	 raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 2:No such file or directory (Error)
	 raised in ccp4_file_rarch <<<<<<
>>>>>> CCP4 library signal library_file:End of File (Error)
	 raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 2:No such file or directory (Error)
	 raised in ccp4_file_readint <<<<<<
>>>>>> System signal 2:No such file or directory (Error)
	 raised in ccp4_file_read <<<<<<
>>>>>> CCP4 library signal library_file:End of File (Error)
	 raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 2:No such file or directory (Error)
	 raised in ccp4_file_readchar <<<<<<
>>>>>> CCP4 library signal mtz:Read failed (Error)
	 raised in MtzGet <<<<<<
INFO:: not an mtz file: /lmb/home/pemsley/data/greg-data/broken.mtz
   got status:  ()
ok
test08_0 (__main__.PdbMtzTestFunctions)
Map Sigma ...    INFO:: map sigmas 0.311501026154 False
ok
test09_0 (__main__.PdbMtzTestFunctions)
Another Level Test ... INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.045 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.035 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.04 seconds for contour map
INFO:: 0.128 seconds in total
INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0  0.00  0.00)
INFO:: Command: (another-level-from-map-molecule-number 2)
ok
test09_1 (__main__.PdbMtzTestFunctions)
db-main makes mainchain ... INFO:: Command: (handle-read-draw-molecule-with-recentre "." 1)
WARNING:: Error reading .
. is a directory.
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 4 read successfully
DEBUG:: there were 0 types with no dictionary 
/lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures successfully opened
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
172 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
20 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
14 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
318 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
208 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
119 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
294 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
131 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
54 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
494 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
64 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
136 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
75 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
247 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
326 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
4 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
411 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
137 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
520 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
205 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
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149 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
140 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
143 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
51 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
123 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
142 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
127 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
106 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
29 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
145 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
72 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
24 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
226 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
228 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
174 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
9 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
45 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
33 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
543 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
23 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
218 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
56 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb
There was an error reading /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb. 
ERROR 42 READ: Duplicate sequence number and insertion code.
         LINE #868
     ATOM    414  CA BSER A  22       6.034  13.399  -2.687  0.21  1.55           C  

Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
171 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
129 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
364 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
13 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
349 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
35 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
155 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
52 fragments garnered from /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
INFO:: 8375 fragments found in total       of which 0 were 5 peptides 
target fragment start res: 10 had 29 db fragment hits, ilength=6
target fragment start res: 13 had 1772 db fragment hits, ilength=6
breaking out of match_target_fragment 6 with iresno= 16
merge fragments 10 to 20 with 2 fit sets to merge
The merging is complete
mainchain_fragment from 10 to 20
done mainchain_fragment
successfully set cell and symmetry
Symmetry available for this molecule
INFO:: Command: (db-mainchain 4 "A" 10 20 "forward")
ok
test10_0 (__main__.PdbMtzTestFunctions)
Set Atom Atribute Test ... INFO:: Command: (set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.50)
ok
test11_0 (__main__.PdbMtzTestFunctions)
Add Terminal Residue Test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 83/90
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 6 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Masking around 41 atoms
fitting terminal residue with 1000 random trials
--- in best_fit_phi_psi() with offset -1
INFO:: Fitting terminal residue  without individual rigid body fitting.
--- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000
                     called fit_terminal_residue_generic() residue-seqnum: 1 offset: -1
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:13:59_2016_modification_0.pdb.gz
INFO:: Command: (add-terminal-residue 6 "A" 1 1)
INFO:: Command: (write-pdb-file 6 "regression-test-terminal-residue.pdb")
INFO:: Command: (handle-read-draw-molecule-with-recentre "regression-test-terminal-residue.pdb" 1)
INFO:: Reading coordinate file: regression-test-terminal-residue.pdb
 PDB file regression-test-terminal-residue.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 83/91
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 7 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
INFO:: Command: (update-go-to-atom-window-on-new-mol)
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: backup file coot-backup/atom_selection_from_regression-test-terminal-residue.pdb_Tue_Dec_27_04:13:59_2016_modification_0.pdb.gz
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
ok
test11_1 (__main__.PdbMtzTestFunctions)
Adding residue by phi psi, no crash ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/frag-2wot.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/frag-2wot.pdb
 PDB file /lmb/home/pemsley/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 9 read successfully
DEBUG:: there were 0 types with no dictionary 
WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276
ok
test12_0 (__main__.PdbMtzTestFunctions)
Select by Sphere ... Symmetry available for this molecule
INFO:: Command: (n-chains 10)
INFO:: Command: (chain_id 10 0)
   Sphere mol: there are 4 residues in chain B
INFO:: Command: (resname-from-serial-number 10 "B" 0)
INFO:: Command: (setnum-from-serial-number 10 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 10 "B" 0)
INFO:: Command: (resname-from-serial-number 10 "B" 1)
INFO:: Command: (setnum-from-serial-number 10 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 10 "B" 1)
INFO:: Command: (resname-from-serial-number 10 "B" 2)
INFO:: Command: (setnum-from-serial-number 10 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 10 "B" 2)
INFO:: Command: (resname-from-serial-number 10 "B" 3)
INFO:: Command: (setnum-from-serial-number 10 "B" 3)
INFO:: Command: (insertion-code-from-serial-number 10 "B" 3)
Found 20 sphere atoms
ok
test13_0 (__main__.PdbMtzTestFunctions)
Test Views ... INFO:: Command: (go-to-view-number 0 1)
ok
test13_1 (__main__.PdbMtzTestFunctions)
Delete Residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 11 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:00_2016_modification_0.pdb.gz
INFO:: Command: (delete-residue 11 "A" 42 "")
residue info (should be False): False
ok
test14_0 (__main__.PdbMtzTestFunctions)
Label Atoms and Delete ... Symmetry available for this molecule
INFO:: Command: (update-go-to-atom-window-on-new-mol)
INFO:: Command: (set-rotation-centre 31.46 21.41 14.82)
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:14:00_2016_modification_0.pdb.gz
INFO:: Command: (delete-residue 12 "B" 10 "")
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:14:00_2016_modification_1.pdb.gz
INFO:: Command: (delete-residue 12 "B" 11 "")
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:14:00_2016_modification_2.pdb.gz
INFO:: Command: (delete-residue 12 "B" 12 "")
ok
test15_0 (__main__.PdbMtzTestFunctions)
Rotamer outliers ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb
 PDB file /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 13 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 ""]
ok
test16_0 (__main__.PdbMtzTestFunctions)
Alt Conf Occ Sum Reset ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/res098.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/res098.pdb
 PDB file /lmb/home/pemsley/data/greg-data/res098.pdb has been read.
Spacegroup: P 41 21 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 14 read successfully
DEBUG:: there were 0 types with no dictionary 
   For atom  CE  A returning occ 0.7
   For atom  CE  B returning occ 0.2
   For atom  NZ  A returning occ 0.7
   For atom  NZ  B returning occ 0.2
created 6 bond       restraints 
created 6 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 13 restraints

INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints: 
   2 bond    links
   7 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 9 non-bonded restraints
initial distortion_score: 26.6475
    Initial RMS Z values
bonds:      0.22918
angles:     0.43392
torsions:   N/A 
planes:     0.322152
non-bonded: 0
chiral vol: 0.162676
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 143) at 9.94487
    Final Estimated RMS Z Scores:
bonds:      0.0950944
angles:     0.665383
torsions:   N/A 
planes:     0.649011
non-bonded: 0
chiral vol: 0.590664
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 3.639
debug:: restraints results 1 5 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_res098.pdb_Tue_Dec_27_04:14:01_2016_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
   For atom  CE  A returning occ 0.7
   For atom  CE  B returning occ 0.2
   For atom  NZ  A returning occ 0.7
   For atom  NZ  B returning occ 0.2
ok
test16_1 (__main__.PdbMtzTestFunctions)
Correct occupancies after auto-fit rotamer on alt-confed residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 15 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.048 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.036 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.04 seconds for contour map
INFO:: 0.132 seconds in total
here in split_residue() 
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:01_2016_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0 
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:01_2016_modification_1.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 11.9313
INFO:: Command: (auto-fit-best-rotamer 93 "A" "" "A" 15 16 1  0.01)
ok
test16_2 (__main__.PdbMtzTestFunctions)
Rotamers work on MSE ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb3knw.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3knw.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb3knw.ent has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 30 links
Symmetry available for this molecule
INFO:: NCS chain comparison 185/199
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 17 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3knw.ent_Tue_Dec_27_04:14:01_2016_modification_0.pdb.gz
    se_1: [['SE  ', ''], [0.7, 2.0, 'SE', ''], [58.8, 66.533, 0.047]]
    se_2: [['SE  ', ''], [0.7, 2.0, 'SE', ''], [60.13112002923666, 69.34847968524429, -0.673518803101735]]
ok
test16_3 (__main__.PdbMtzTestFunctions)
Hs are correctly swapped on a TYR ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 91/204
INFO:: NCS chain comparison 90/204
INFO:: NCS chain comparison 175/179
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain B"
Molecule 18 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/_lmb_home_pemsley_data_greg-data_pdb1py3.ent_Tue_Dec_27_04:14:02_2016_modification_0.pdb.gz
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 30 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 35 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 39 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "A" 54 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 57 ""] PHE
INFO:: (result) ASP swapped atoms in [spec: 1 "A" 66 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "A" 90 ""] PHE
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 2 ""] ASP
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 30 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 35 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 39 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 54 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "B" 77 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "B" 85 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "B" 90 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 30 ""] TYR
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 32 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "C" 35 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "C" 39 ""] PHE
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 54 ""] TYR
INFO:: (result) PHE swapped atoms in [spec: 1 "C" 57 ""] PHE
INFO:: (result) TYR swapped atoms in [spec: 1 "C" 81 ""] TYR
INFO:: (result) ASP swapped atoms in [spec: 1 "C" 85 ""] ASP
INFO:: (result) PHE swapped atoms in [spec: 1 "C" 90 ""] PHE
INFO:: (result) ASP swapped atoms in [spec: 1 "C" 94 ""] ASP
INFO:: 25 residues had their atoms swapped
BL DEBUG:: results: [True, True, True, True]
ok
test16_4 (__main__.PdbMtzTestFunctions)
Splitting residue leaves no atoms with negative occupancy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 19 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.049 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.036 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.04 seconds for contour map
INFO:: 0.132 seconds in total
INFO:: Command: (zero-occupancy-residue-range 19 "A" 37 37)
here in split_residue() 
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:02_2016_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0 
INFO:: Command: (close-molecule 19)
INFO:: Command: (close-molecule 20)
ok
test17_0 (__main__.PdbMtzTestFunctions)
Pepflip flips the correct alt confed atoms ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb
 PDB file /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 21 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-pepflip-test.pdb_Tue_Dec_27_04:14:02_2016_modification_0.pdb.gz
flipped 65 A
ok
test18_0 (__main__.PdbMtzTestFunctions)
Correction of CISPEP test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 22 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (go-to-view-number 1 1)
in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x22f0c3d0
omega: 1 12.7704 degrees 
INFO This is a CIS peptide - making it TRANS
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:14:02_2016_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:14:02_2016_modification_1.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 11 A 12 
flipped 11 A
INFO:: mutate 11 A to a GLY
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:14:02_2016_modification_2.pdb.gz
INFO:: Command: (mutate 22 "A" 11 "" "GLY")
created 10 bond       restraints 
created 10 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 21 restraints

INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A
Link restraints: 
   1 bond    links
   4 angle   links
   2 plane   links
   1 trans-peptide links
   0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints: 
   2 bond    links
   7 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 27 non-bonded restraints
initial distortion_score: 4133.64
    Initial RMS Z values
bonds:      15.4585
angles:     7.12423
torsions:   N/A 
planes:     2.18109
non-bonded: 126.244
chiral vol: 3.04463
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 2) at -4889.43
    Final Estimated RMS Z Scores:
bonds:      0.885096
angles:     0.76878
torsions:   N/A 
planes:     2.52474
non-bonded: 0.218649
chiral vol: 0.384742
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 5.328
Refinement elapsed time: 0.019
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:14:02_2016_modification_3.pdb.gz
INFO:: replace_coords: 11 atoms updated.
INFO:: mutate 11 A to a LEU
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:14:02_2016_modification_4.pdb.gz
INFO:: Command: (mutate 22 "A" 11 "" "LEU")
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:14:02_2016_modification_5.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 8.6831
INFO:: Command: (auto-fit-best-rotamer 11 "" "" "A" 22 2 1  1.00)
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
created 14 bond       restraints 
created 16 angle      restraints 
created 0 plane      restraints 
created 2 chiral vol restraints 
created 32 restraints

INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A
Link restraints: 
   1 bond    links
   4 angle   links
   2 plane   links
   1 trans-peptide links
   0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints: 
   2 bond    links
   7 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 63 non-bonded restraints
initial distortion_score: -6042.29
    Initial RMS Z values
bonds:      0.907898
angles:     1.59917
torsions:   N/A 
planes:     3.04062
non-bonded: 0.611102
chiral vol: 0.415505
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 98) at -6164.55
    Final Estimated RMS Z Scores:
bonds:      0.870654
angles:     0.71055
torsions:   N/A 
planes:     2.58034
non-bonded: 0.100151
chiral vol: 0.222079
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 5.475
Refinement elapsed time: 0.019
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Tue_Dec_27_04:14:02_2016_modification_6.pdb.gz
INFO:: replace_coords: 15 atoms updated.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: Command: (write-pdb-file 22 "tmp-fixed-cis.pdb")
ok
test19_0 (__main__.PdbMtzTestFunctions)
Refine Zone with Alt conf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 23 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.048 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.035 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.039 seconds for contour map
INFO:: 0.13 seconds in total
created 5 bond       restraints 
created 4 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 10 restraints

INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 6 non-bonded restraints
initial distortion_score: -2777.33
    Initial RMS Z values
bonds:      1.67379
angles:     1.06965
torsions:   N/A 
planes:     0.611295
non-bonded: 9.24559
chiral vol: 1.46202
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 86) at -2899.61
    Final Estimated RMS Z Scores:
bonds:      1.07327
angles:     1.21001
torsions:   N/A 
planes:     0.378537
non-bonded: 3.39317
chiral vol: 0.705494
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 5.846
Refinement elapsed time: 0.009
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:03_2016_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
   refined moved: d= 0.227112928852
ok
test20_0 (__main__.PdbMtzTestFunctions)
Sphere Refine ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 83/90
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 25 read successfully
DEBUG:: there were 0 types with no dictionary 
here in split_residue() 
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:14:03_2016_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0 
INFO:: Command: (set-go-to-atom-molecule 25)
   imol: 25 residues: [['A', 93, ''], ['A', 92, ''], ['A', 3, ''], ['A', 5, '']]
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 1311 non-bonded restraints
initial distortion_score: -20878.7
    Initial RMS Z values
bonds:      1.74258
angles:     1.26763
torsions:   N/A 
planes:     0.838264
non-bonded: 0.000805435
chiral vol: 0.894378
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 112) at -21302.6
    Final Estimated RMS Z Scores:
bonds:      1.12964
angles:     0.734137
torsions:   N/A 
planes:     0.608926
non-bonded: 0
chiral vol: 0.27658
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.325
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:14:03_2016_modification_1.pdb.gz
INFO:: replace_coords: 39 atoms updated.
   imol: 25 residues: [['A', 41, ''], ['A', 42, ''], ['A', 40, ''], ['A', 39, ''], ['A', 43, '']]
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 1031 non-bonded restraints
initial distortion_score: -7315.05
    Initial RMS Z values
bonds:      0.980695
angles:     1.01754
torsions:   N/A 
planes:     1.78749
non-bonded: 6.40492
chiral vol: 10.2816
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 99) at -15843.9
    Final Estimated RMS Z Scores:
bonds:      1.98493
angles:     1.86721
torsions:   N/A 
planes:     1.56667
non-bonded: 0.065536
chiral vol: 1.81675
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.673
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Tue_Dec_27_04:14:03_2016_modification_2.pdb.gz
INFO:: replace_coords: 41 atoms updated.
======= got bond length 1.28867658809
ok
test20_1 (__main__.PdbMtzTestFunctions)
Refinement gives useful results ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 26 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.048 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.034 seconds for FFT
INFO:: 0.006 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.038 seconds for contour map
INFO:: 0.127 seconds in total
created 29 bond       restraints 
created 32 angle      restraints 
created 2 plane      restraints 
created 4 chiral vol restraints 
created 67 restraints

INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A
Link restraints: 
   3 bond    links
   9 angle   links
   6 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 315 non-bonded restraints
initial distortion_score: -6040.02
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     1.98457
non-bonded: 11.389
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 113) at -11674.9
    Final Estimated RMS Z Scores:
bonds:      1.88942
angles:     1.81724
torsions:   N/A 
planes:     2.00256
non-bonded: 0.0933873
chiral vol: 1.93418
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 7.15
Refinement elapsed time: 0.095
   refinement results: ['', 0, [['Bonds', 'Bonds:    1.889', 1.889420986175537], ['Angles', 'Angles:   1.817', 1.8172374963760376], ['Planes', 'Planes:   2.003', 2.0025599002838135], ['Non-bonded', 'Non-bonded:   0.306', 0.3055934011936188], ['Chirals', 'Chirals:   1.934', 1.9341847896575928]]]
::::   ow factor 1.91085079312
   INFO:: setting refinement weight to 16.432275081 from 60.0 / ( 1.91085079312 * 1.91085079312 )
created 29 bond       restraints 
created 32 angle      restraints 
created 2 plane      restraints 
created 4 chiral vol restraints 
created 67 restraints

INFO:: GetSelIndex (make_link_restraints) returned 4 residues (for link restraints) between (and including) residues 40 and 43 of chain A
Link restraints: 
   3 bond    links
   9 angle   links
   6 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints)
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 315 non-bonded restraints
initial distortion_score: 1830.71
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     1.98457
non-bonded: 11.389
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 2) at -3125.7
    Final Estimated RMS Z Scores:
bonds:      0.681408
angles:     0.825836
torsions:   N/A 
planes:     1.6896
non-bonded: 0.00535214
chiral vol: 0.793652
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 7.428
Refinement elapsed time: 0.277
   refinement results: ['', 0, [['Bonds', 'Bonds:    0.681', 0.6814079880714417], ['Angles', 'Angles:   0.826', 0.8258360624313354], ['Planes', 'Planes:   1.690', 1.6895984411239624], ['Non-bonded', 'Non-bonded:   0.073', 0.07315830886363983], ['Chirals', 'Chirals:   0.794', 0.7936520576477051]]]
::::   ow factor 0.997623637319
ok
test21_0 (__main__.PdbMtzTestFunctions)
Rigid Body Refine Alt Conf Waters ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb
 PDB file /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 28 read successfully
DEBUG:: there were 0 types with no dictionary 
masking....masking done
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_alt-conf-waters.pdb_Tue_Dec_27_04:14:05_2016_modification_0.pdb.gz
INFO:: replace_coords: 1 atoms updated.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
ok
test22_0 (__main__.PdbMtzTestFunctions)
Setting multiple atom attributes ... ok
test23_0 (__main__.PdbMtzTestFunctions)
Tweak Alt Confs on Active Residue ... INFO:: Command: (update-go-to-atom-window-on-other-molecule-chosen)
INFO:: Command: (set-go-to-atom-molecule 0)
INFO:: Command: (set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B")
ok
test24_0 (__main__.PdbMtzTestFunctions)
Backrub rotamer ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb" 0)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb
 PDB file /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 29 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
INFO:: Command: (copy-molecule 29)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Tue_Dec_27_04:14:05_2016_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Tue_Dec_27_04:14:05_2016_modification_1.pdb.gz
INFO:: replace_coords: 14 atoms updated.
ok
test25_0 (__main__.PdbMtzTestFunctions)
Libcif horne ... ok
test26_0 (__main__.PdbMtzTestFunctions)
Refmac Parameters Storage ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "/RNASE3GMP/COMPLEX/FWT" "/RNASE3GMP/COMPLEX/PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.046 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.035 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.037 seconds for contour map
INFO:: 0.126 seconds in total
INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible.
ok
test26_1 (__main__.PdbMtzTestFunctions)
OXT is added before TER record - add only one ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb
 PDB file /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 32 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_test-TER-OXT.pdb_Tue_Dec_27_04:14:06_2016_modification_0.pdb.gz
Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45
INFO:: Command: (add-OXT-to-residue 32 14 "" "A")
WARNING:: This residue already has an OXT - aborting
INFO:: Command: (add-OXT-to-residue 32 14 "" "A")
INFO:: Command: (write-pdb-file 32 "test-TER-OXT-added.pdb")
   found TER TER      25      ASP A  14                                                      

ok
test27_0 (__main__.PdbMtzTestFunctions)
The position of the oxygen after a mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/val.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/val.pdb
 PDB file /lmb/home/pemsley/data/greg-data/val.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 33 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: mutate 3 C to a HIS
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_val.pdb_Tue_Dec_27_04:14:06_2016_modification_0.pdb.gz
INFO:: Command: (mutate 33 "C" 3 "" "HIS")
INFO:: Command: (write-pdb-file 33 "his.pdb")
ok
test27_1 (__main__.PdbMtzTestFunctions)
TER is at the end of a nucleotide after mutation ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2yie-frag.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2yie-frag.pdb
 PDB file /lmb/home/pemsley/data/greg-data/2yie-frag.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 34 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2yie-frag.pdb_Tue_Dec_27_04:14:06_2016_modification_0.pdb.gz
INFO:: 6 matched atoms had: 
   mean devi: 0.0404315
    rms devi: 0.0471732
    max devi: 0.0832785
    min devi: 0.0130055
INFO:: Command: (mutate-base 34 "X" 54 "" "C")
INFO:: Command: (write-pdb-file 34 "2yie-mutated.pdb")
ok
test27_2 (__main__.PdbMtzTestFunctions)
C7 is removed on mutation from a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/4f8g.pdb
 PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 35 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Tue_Dec_27_04:14:06_2016_modification_0.pdb.gz
INFO:: 6 matched atoms had: 
   mean devi: 0.0434566
    rms devi: 0.0477873
    max devi: 0.073989
    min devi: 0.0147744
INFO:: Command: (mutate-base 35 "A" 19 "" "DC")
INFO:: Command: (write-pdb-file 35 "test-1.pdb")
ok
test27_3 (__main__.PdbMtzTestFunctions)
C7 is added on mutation to a DC ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/4f8g.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/4f8g.pdb
 PDB file /lmb/home/pemsley/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 36 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_4f8g.pdb_Tue_Dec_27_04:14:06_2016_modification_0.pdb.gz
INFO:: 6 matched atoms had: 
   mean devi: 0.0394451
    rms devi: 0.0444615
    max devi: 0.0694865
    min devi: 0.0151341
INFO:: Command: (mutate-base 36 "A" 10 "" "DT")
INFO:: Command: (write-pdb-file 36 "test-2.pdb")
ok
test28_0 (__main__.PdbMtzTestFunctions)
Deleting (non-existing) Alt conf and Go To Atom [JED] ... failed to delete residue atoms A 88 :A:
INFO:: Command: (delete-residue-with-full_spec 0 1 "A" 88 "" "A")
ok
test29_0 (__main__.PdbMtzTestFunctions)
Mask and difference map ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.048 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.034 seconds for FFT
INFO:: 0.008 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.031 seconds for contour map
INFO:: 0.122 seconds in total
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.047 seconds to read MTZ file
INFO:: 0.05 seconds to initialize map
INFO:: 0.05 seconds for FFT
INFO:: 0.012 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.052 seconds for contour map
INFO:: 0.211 seconds in total
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 0)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 39 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Masking around 64 atoms
Map statistics: mean: -0.00140371 st.d: 0.305546
Map statistics: min: -0.895738, max: 2.76376
 -0.849994    7
 -0.758507    47
  -0.66702    345
 -0.575532    1966
 -0.484045    7547
 -0.392558    21145
  -0.30107    36984
 -0.209583    49747
 -0.118095    62502
-0.0266081    78146
 0.0648793    56227
  0.156367    31741
  0.247854    15372
  0.339341    9396
  0.430829    7278
  0.522316    6354
  0.613803    5287
  0.705291    4622
  0.796778    3865
  0.888266    3168
  0.979753    2366
   1.07124    1769
   1.16273    1258
   1.25421    879
    1.3457    637
   1.43719    417
   1.52868    237
   1.62016    135
   1.71165    69
   1.80314    46
   1.89463    18
   1.98611    8
    2.0776    2
   2.16909    6
   2.26058    2
   2.35206    0
   2.44355    1
   2.53504    3
   2.62653    0
   2.71801    1
    2.8095    0
INFO:: Command: (atom_info_string 39 A 20   CA  )
INFO:: Command: (atom_info_string 39 A 21   CA  )
INFO:: Command: (atom_info_string 39 A 22   CA  )
INFO:: Command: (atom_info_string 39 A 23   CA  )
INFO:: Command: (atom_info_string 39 A 24   CA  )
INFO:: Command: (atom_info_string 39 A 25   CA  )
INFO:: Command: (atom_info_string 39 A 26   CA  )
INFO:: Command: (atom_info_string 39 A 27   CA  )
INFO:: Command: (atom_info_string 39 A 28   CA  )
INFO:: Command: (atom_info_string 39 A 29   CA  )
INFO:: Command: (atom_info_string 39 A 30   CA  )
INFO:: Command: (atom_info_string 39 A 1   CA  )
INFO:: Command: (atom_info_string 39 A 2   CA  )
INFO:: Command: (atom_info_string 39 A 3   CA  )
INFO:: Command: (atom_info_string 39 A 4   CA  )
INFO:: Command: (atom_info_string 39 A 5   CA  )
INFO:: Command: (atom_info_string 39 A 6   CA  )
INFO:: Command: (atom_info_string 39 A 7   CA  )
INFO:: Command: (atom_info_string 39 A 8   CA  )
INFO:: Command: (atom_info_string 39 A 9   CA  )
INFO:: Command: (atom_info_string 39 A 10   CA  )
   high-values: [0.7880393266677856, 0.9311162233352661, 0.9948474168777466, 1.0713924169540405, 0.7348382472991943, 0.8019416332244873, 0.6376814842224121, 0.6461937427520752, 0.9521262645721436, 0.9289177656173706, 0.966407835483551]  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: -0.001364 st.d: 0.0602937
Map statistics: min: -2.97717, max: 0.74609
  -2.93063    1
  -2.83755    1
  -2.74447    1
  -2.65139    2
  -2.55831    2
  -2.46522    0
  -2.37214    2
  -2.27906    1
  -2.18598    1
   -2.0929    4
  -1.99982    2
  -1.90673    3
  -1.81365    4
  -1.72057    4
  -1.62749    8
  -1.53441    11
  -1.44133    15
  -1.34825    33
  -1.25516    33
  -1.16208    49
    -1.069    65
 -0.975919    120
 -0.882838    145
 -0.789756    159
 -0.696674    202
 -0.603593    249
 -0.510511    275
  -0.41743    291
 -0.324348    411
 -0.231267    440
 -0.138185    581
-0.0451034    300768
 0.0479782    101975
   0.14106    1213
  0.234141    1098
  0.327223    767
  0.420304    463
  0.513386    156
  0.606468    36
  0.699549    9
  0.792631    0
   diff-high-values: [0.003214021911844611, 0.005670727230608463, 0.003183471504598856, 0.003650454105809331, 0.005187041126191616, 0.00335022434592247, 0.0024678956251591444, 0.007025350350886583, 0.004253414925187826, -0.0006197408074513078, 0.003509128000587225]  diff-low-values: [-0.5327255725860596, -0.93985915184021, -0.7048763632774353, -0.827702522277832, -0.8482539653778076, -1.0417752265930176, -1.1633360385894775, -1.185960292816162, -0.8826918601989746, -0.8691443800926208]
ok
test29_1 (__main__.PdbMtzTestFunctions)
Skeletonize a map ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 42 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.047 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.034 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.039 seconds for contour map
INFO:: 0.128 seconds in total
INFO:: Command: (close-molecule 42)
INFO:: Command: (close-molecule 43)
ok
test29_2 (__main__.PdbMtzTestFunctions)
Simple Averaged maps ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.8
INFO grid sampling...Nuvw = ( 128, 160,  80)
INFO:: 0.048 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.035 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ 8.97066e-10
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.0144
      Map minimum: ..... -0.895738
INFO:: 0.037 seconds for contour map
INFO:: 0.127 seconds in total
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 2.5
INFO grid sampling...Nuvw = ( 180, 216, 108)
INFO:: 0.046 seconds to read MTZ file
INFO:: 0.069 seconds to initialize map
INFO:: 0.065 seconds for FFT
INFO:: 0.015 seconds for statistics
      Map mean: ........ 1.16132e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.07133
      Map minimum: ..... -0.877519
INFO:: 0.081 seconds for contour map
INFO:: 0.276 seconds in total
INFO:: multiplying map (function index) 0 Nuvw = ( 128, 160,  80) by 1
INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1
Map statistics: mean: 1.68726e-07 st.d: 0.311081
Map statistics: min: -0.894093, max: 3.00714
 -0.845327    8
 -0.747797    64
 -0.650266    542
 -0.552735    3067
 -0.455204    12045
 -0.357673    29986
 -0.260143    46658
 -0.162612    61563
-0.0650809    73639
 0.0324499    68489
  0.129981    41912
  0.227511    19494
  0.325042    11050
  0.422573    8221
  0.520104    7074
  0.617635    5839
  0.715166    5071
  0.812696    4183
  0.910227    3295
   1.00776    2384
   1.10529    1722
   1.20282    1175
   1.30035    843
   1.39788    560
   1.49541    325
   1.59294    179
   1.69047    90
     1.788    59
   1.88554    23
   1.98307    9
    2.0806    8
   2.17813    6
   2.27566    2
   2.37319    2
   2.47072    4
   2.56825    3
   2.66578    2
   2.76331    2
   2.86084    1
   2.95837    0
    3.0559    1
Map statistics: mean: -1.67829e-07 st.d: 0.00107626
Map statistics: min: -0.0109431, max: 0.0109034
  -0.01067    1
-0.0101239    1
-0.00957771    0
-0.00903155    1
-0.00848539    3
-0.00793922    2
-0.00739306    4
-0.0068469    7
-0.00630074    25
-0.00575458    37
-0.00520842    103
-0.00466225    260
-0.00411609    640
-0.00356993    1269
-0.00302377    2611
-0.00247761    5434
-0.00193144    10529
-0.00138528    21798
-0.000839121    51978
-0.000292959    109494
0.000253203    110466
0.000799365    52014
0.00134553    20447
0.00189169    9607
0.00243785    5235
0.00298401    2974
0.00353017    1857
0.00407634    1167
 0.0046225    683
0.00516866    388
0.00571482    223
0.00626098    139
0.00680714    86
0.00735331    56
0.00789947    25
0.00844563    16
0.00899179    7
0.00953795    4
 0.0100841    4
 0.0106303    4
 0.0111764    1
  INFO:: map sigmas: normal 0.311081498861 and diff-map: 0.00107625499368
ok
test30_0 (__main__.PdbMtzTestFunctions)
Make a glycosidic linkage ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb
 PDB file /lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 48 read successfully
DEBUG:: there were 2 types with no dictionary 
   bond-length:  2.97694071154
created 46 bond       restraints 
created 82 angle      restraints 
created 2 plane      restraints 
created 8 chiral vol restraints 
created 138 restraints

INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A
INFO:: glycosidic_linkage type :ALPHA1-4:
Link restraints: 
   1 bond    links
   3 angle   links
   0 plane   links
   0 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 671 non-bonded restraints
initial distortion_score: 7132.61
    Initial RMS Z values
bonds:      11.3589
angles:     3.25886
torsions:   N/A 
planes:     0.0835273
non-bonded: 0.237255
chiral vol: 0.903463
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 345) at 0.372095
    Final Estimated RMS Z Scores:
bonds:      0.00617166
angles:     0.0648855
torsions:   N/A 
planes:     0.000687124
non-bonded: 1.34874e-07
chiral vol: 0.0392937
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 12.441
debug:: restraints results 1 5 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_multi-carbo-coot-2.pdb_Tue_Dec_27_04:14:10_2016_modification_0.pdb.gz
INFO:: replace_coords: 46 atoms updated.
   bond-length:  1.43915408366
ok
test30_1 (__main__.PdbMtzTestFunctions)
Refine an NAG-ASN Link ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb
 PDB file /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 3 links
Symmetry available for this molecule
INFO:: NCS chain comparison 4/110
Molecule 49 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.049 seconds to read MTZ file
INFO:: 0.016 seconds to initialize map
INFO:: 0.027 seconds for FFT
INFO:: 0.004 seconds for statistics
      Map mean: ........ 1.06932e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.028 seconds for contour map
INFO:: 0.124 seconds in total
reading /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/share/coot/NAG-decorations.tab
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:14:11_2016_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:14:11_2016_modification_1.pdb.gz
INFO:: link torsion generated from link bond restraint
DEBUG tosion quads:  0 [spec: model 1 "B" 464 "" " C2 " ""] [spec: model 1 "B" 464 "" " C1 " ""] [spec: model 1 "B" 141 "" " ND2" ""] [spec: model 1 "B" 141 "" " CG " ""] "Bond-derived synthetic torsion-phi-0" torsion: 128.493
DEBUG tosion quads:  1 [spec: model 1 "B" 141 "" " N  " ""] [spec: model 1 "B" 141 "" " CA " ""] [spec: model 1 "B" 141 "" " CB " ""] [spec: model 1 "B" 141 "" " CG " ""] "chi1" torsion: -169.592
DEBUG tosion quads:  2 [spec: model 1 "B" 141 "" " CA " ""] [spec: model 1 "B" 141 "" " CB " ""] [spec: model 1 "B" 141 "" " CG " ""] [spec: model 1 "B" 141 "" " ND2" ""] "chi2" torsion: 179.253
DEBUG tosion quads:  3 [spec: model 1 "B" 464 "" " O5 " ""] [spec: model 1 "B" 464 "" " C5 " ""] [spec: model 1 "B" 464 "" " C6 " ""] [spec: model 1 "B" 464 "" " O6 " ""] "var_3" torsion: -56.0926
DEBUG tosion quads:  4 [spec: model 1 "B" 464 "" " C3 " ""] [spec: model 1 "B" 464 "" " C2 " ""] [spec: model 1 "B" 464 "" " N2 " ""] [spec: model 1 "B" 464 "" " C7 " ""] "var_11" torsion: -144.423
---- contact_info() constructor added link bond contact 8 7
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:14:11_2016_modification_2.pdb.gz
INFO:: replace_coords: 22 atoms updated.
INFO:: created 55 restraints

created 21 bond       restraints 
created 27 angle      restraints 
created 2 plane      restraints 
created 5 chiral vol restraints 
Link restraints: 
   1 bond    links
   2 angle   links
   1 plane   links
   0 trans-peptide links
   0 parallel plane restraints
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 666 non-bonded restraints
initial distortion_score: 105713
    Initial RMS Z values
bonds:      0.360748
angles:     0.606408
torsions:   N/A 
planes:     0.68341
non-bonded: 159.864
chiral vol: 0.444926
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 104) at -393.932
    Final Estimated RMS Z Scores:
bonds:      2.12671
angles:     2.1485
torsions:   N/A 
planes:     0.585802
non-bonded: 0.0994778
chiral vol: 1.62498
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 13.979
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:14:11_2016_modification_3.pdb.gz
INFO:: replace_coords: 22 atoms updated.
INFO:: link torsion generated from link bond restraint
DEBUG tosion quads:  0 [spec: model 1 "B" 464 "" " C2 " ""] [spec: model 1 "B" 464 "" " C1 " ""] [spec: model 1 "B" 141 "" " ND2" ""] [spec: model 1 "B" 141 "" " CG " ""] "Bond-derived synthetic torsion-phi-0" torsion: 155.924
DEBUG tosion quads:  1 [spec: model 1 "B" 141 "" " N  " ""] [spec: model 1 "B" 141 "" " CA " ""] [spec: model 1 "B" 141 "" " CB " ""] [spec: model 1 "B" 141 "" " CG " ""] "chi1" torsion: -165.2
DEBUG tosion quads:  2 [spec: model 1 "B" 141 "" " CA " ""] [spec: model 1 "B" 141 "" " CB " ""] [spec: model 1 "B" 141 "" " CG " ""] [spec: model 1 "B" 141 "" " ND2" ""] "chi2" torsion: 173.934
DEBUG tosion quads:  3 [spec: model 1 "B" 464 "" " O5 " ""] [spec: model 1 "B" 464 "" " C5 " ""] [spec: model 1 "B" 464 "" " C6 " ""] [spec: model 1 "B" 464 "" " O6 " ""] "var_3" torsion: 134.208
DEBUG tosion quads:  4 [spec: model 1 "B" 464 "" " C3 " ""] [spec: model 1 "B" 464 "" " C2 " ""] [spec: model 1 "B" 464 "" " N2 " ""] [spec: model 1 "B" 464 "" " C7 " ""] "var_11" torsion: -155.031
---- contact_info() constructor added link bond contact 8 7
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:14:11_2016_modification_4.pdb.gz
INFO:: replace_coords: 22 atoms updated.
INFO:: created 55 restraints

created 21 bond       restraints 
created 27 angle      restraints 
created 2 plane      restraints 
created 5 chiral vol restraints 
Link restraints: 
   1 bond    links
   2 angle   links
   1 plane   links
   0 trans-peptide links
   0 parallel plane restraints
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 622 non-bonded restraints
initial distortion_score: 1349.87
    Initial RMS Z values
bonds:      2.12671
angles:     2.1485
torsions:   N/A 
planes:     0.585802
non-bonded: 3.09365
chiral vol: 1.62498
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 99) at -443.857
    Final Estimated RMS Z Scores:
bonds:      2.12346
angles:     2.26936
torsions:   N/A 
planes:     0.921659
non-bonded: 0.107452
chiral vol: 1.63188
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 14.537
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:14:11_2016_modification_5.pdb.gz
INFO:: replace_coords: 22 atoms updated.
INFO:: created 55 restraints

created 21 bond       restraints 
created 27 angle      restraints 
created 2 plane      restraints 
created 5 chiral vol restraints 
Link restraints: 
   1 bond    links
   2 angle   links
   1 plane   links
   0 trans-peptide links
   0 parallel plane restraints
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   2 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 640 non-bonded restraints
initial distortion_score: 119.038
    Initial RMS Z values
bonds:      2.12346
angles:     2.26936
torsions:   N/A 
planes:     0.921659
non-bonded: 0.983954
chiral vol: 1.63188
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 74) at -393.932
    Final Estimated RMS Z Scores:
bonds:      2.12676
angles:     2.14861
torsions:   N/A 
planes:     0.585944
non-bonded: 0.103531
chiral vol: 1.62547
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 14.678
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Tue_Dec_27_04:14:11_2016_modification_6.pdb.gz
INFO:: replace_coords: 22 atoms updated.
ok
test31_0 (__main__.PdbMtzTestFunctions)
Test for flying hydrogens on undo ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-VAL.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 51 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: found bad VAL chiral atom: A 1   CB  
created 14 bond       restraints 
created 25 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 40 restraints

INFO:: make_restraints(): made 44 non-bonded restraints
initial distortion_score: 4.99701
    Initial RMS Z values
bonds:      0.542493
angles:     0.164062
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.451586
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 82) at 0.247695
    Final Estimated RMS Z Scores:
bonds:      0.0111735
angles:     0.0948502
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.145027
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 15.275
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:14:13_2016_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: undo molecule number set to: 51
INFO:: Command: (set-undo-molecule 51)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:14:13_2016_modification_1.pdb.gz
restoring from backup 2 2
INFO:: Reading coordinate file: coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:14:13_2016_modification_0.pdb.gz
 PDB file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:14:13_2016_modification_0.pdb.gz has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2
INFO:: Command: (apply-undo)
created 14 bond       restraints 
created 25 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 40 restraints

INFO:: make_restraints(): made 44 non-bonded restraints
initial distortion_score: 4.99701
    Initial RMS Z values
bonds:      0.542493
angles:     0.164062
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.451586
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 82) at 0.247695
    Final Estimated RMS Z Scores:
bonds:      0.0111735
angles:     0.0948502
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.145027
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 15.326
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Tue_Dec_27_04:14:13_2016_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
ok
test32_0 (__main__.PdbMtzTestFunctions)
Test for mangling of hydrogen names from a PDB v 3.0 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb
 PDB file /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 52 read successfully
DEBUG:: there were 0 types with no dictionary 
created 17 bond       restraints 
created 31 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 49 restraints

INFO:: make_restraints(): made 67 non-bonded restraints
initial distortion_score: 903.063
    Initial RMS Z values
bonds:      5.62114
angles:     3.43297
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.753357
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 184) at 0.473541
    Final Estimated RMS Z Scores:
bonds:      0.00930256
angles:     0.120894
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.13781
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 16.067
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Tue_Dec_27_04:14:13_2016_modification_0.pdb.gz
INFO:: replace_coords: 18 atoms updated.
ok
test32_1 (__main__.PdbMtzTestFunctions)
Correct matching dictionary names from test name ... ok
test33_0 (__main__.PdbMtzTestFunctions)
Update monomer restraints ... looping over restraint
Symmetry available for this molecule
INFO:: Command: (update-go-to-atom-window-on-new-mol)
created 11 bond       restraints 
created 15 angle      restraints 
created 1 plane      restraints 
created 1 chiral vol restraints 
created 28 restraints

INFO:: make_restraints(): made 39 non-bonded restraints
initial distortion_score: 2043.7
    Initial RMS Z values
bonds:      1.1515
angles:     0.847578
torsions:   N/A 
planes:     3.05577
non-bonded: 81.9061
chiral vol: 0.757848
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 48) at -1084.95
    Final Estimated RMS Z Scores:
bonds:      0.822339
angles:     0.602649
torsions:   N/A 
planes:     0.591257
non-bonded: 0.0847814
chiral vol: 0.208046
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 16.139
Refinement elapsed time: 0.022
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:14:13_2016_modification_0.pdb.gz
INFO:: replace_coords: 12 atoms updated.
  Bond-length:  2.60363256424
   pass intermediate 2.8 tolerance test
looping over restraint
created 12 bond       restraints 
created 15 angle      restraints 
created 1 plane      restraints 
created 1 chiral vol restraints 
created 29 restraints

INFO:: make_restraints(): made 36 non-bonded restraints
initial distortion_score: 1373.86
    Initial RMS Z values
bonds:      14.3456
angles:     0.602649
torsions:   N/A 
planes:     0.591257
non-bonded: 0
chiral vol: 0.208046
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 72) at -1184.04
    Final Estimated RMS Z Scores:
bonds:      0.291054
angles:     0.265936
torsions:   N/A 
planes:     0.730056
non-bonded: 0
chiral vol: 0.148355
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 16.166
Refinement elapsed time: 0.016
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:14:13_2016_modification_1.pdb.gz
INFO:: replace_coords: 12 atoms updated.
  OK plane atom   CB 
  Bond-length:  1.51868832076
ok
test33_1 (__main__.PdbMtzTestFunctions)
Write mmCIF restraints correctly ... INFO:: wrote mmCIF "coot-test-ala.cif"
ok
test34_0 (__main__.PdbMtzTestFunctions)
Refinement OK with zero bond esd ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 54 read successfully
DEBUG:: there were 1 types with no dictionary 
Welcome to Coot
looping over restraint
created 5 bond       restraints 
created 9 angle      restraints 
created 1 plane      restraints 
created 0 chiral vol restraints 
created 15 restraints

INFO:: make_restraints(): made 7 non-bonded restraints
initial distortion_score: 4848.17
    Initial RMS Z values
bonds:      0.0119892
angles:     0.00653967
torsions:   N/A 
planes:     0
non-bonded: 689.927
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 76) at -291.4
    Final Estimated RMS Z Scores:
bonds:      0.075214
angles:     0.35914
torsions:   N/A 
planes:     0.119337
non-bonded: 0
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 17.072
Refinement elapsed time: 0.027
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-ACT.pdb_Tue_Dec_27_04:14:14_2016_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
ok
test35_0 (__main__.PdbMtzTestFunctions)
Change Chain IDs and Chain Sorting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 55 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_0.pdb.gz
istat: ; 1
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_1.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 26 A 27 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_2.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_3.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_4.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_5.pdb.gz
INFO:: Removing CIS peptide from PDB header: B 26 B 27 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_6.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_7.pdb.gz
INFO:: Command: (n-chains 55)
INFO:: Command: (chain_id 55 0)
INFO:: Command: (chain_id 55 1)
INFO:: Command: (chain_id 55 2)
INFO:: Command: (chain_id 55 3)
INFO:: Command: (chain_id 55 4)
INFO:: Command: (chain_id 55 5)
INFO:: Command: (chain_id 55 6)
INFO:: Command: (chain_id 55 7)
INFO:: Command: (chain_id 55 8)
ok
test36_0 (__main__.PdbMtzTestFunctions)
Replace Fragment ... Symmetry available for this molecule
INFO:: Command: (copy-molecule 0)
Symmetry available for this molecule
INFO:: Command: (update-go-to-atom-window-on-new-mol)
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:15_2016_modification_0.pdb.gz
INFO:: replace_coords: 1465 atoms updated.
INFO:: Command: (replace-fragement 56 "//A70-80")
   distances:  [20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966, 20.83266665599966]
ok
test37_0 (__main__.PdbMtzTestFunctions)
Residues in Region of Residue ...    found 6 neighbours [['A', 39, ''], ['A', 41, ''], ['A', 38, ''], ['B', 61, ''], ['A', 42, ''], ['B', 60, '']]
   found 0 neighbours []
ok
test38_0 (__main__.PdbMtzTestFunctions)
Residues in region of a point ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 58 read successfully
DEBUG:: there were 0 types with no dictionary 
ok
test39_0 (__main__.PdbMtzTestFunctions)
Empty molecule on type selection ... in new_molecule_by_residue_type_selection Something bad happened - No residues selected
INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected
Residue "TRP" does not exist in molecule 0!?")
in new_molecule_by_residue_type_selection Something bad happened - No residues selected
INFO:: Command: (info-dialog "Oops, failed to select residue type. No residues selected
Residue "TRP" does not exist in molecule 0!?")
ok
test40_0 (__main__.PdbMtzTestFunctions)
Set Rotamer ... INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:16_2016_modification_0.pdb.gz
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
ok
test41_0 (__main__.PdbMtzTestFunctions)
Rotamer names and scores are correct ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 59 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (turn-off-backup 59)
INFO:: Command: (rotamer-score 59 "A" 28 "")
   Rotamer 0 : m-85 100.0
INFO:: Command: (rotamer-score 59 "A" 28 "")
   Rotamer 1 : t80 90.1668395996
INFO:: Command: (rotamer-score 59 "A" 28 "")
   Rotamer 2 : p90 50.7077865601
INFO:: Command: (rotamer-score 59 "A" 28 "")
   Rotamer 3 : m -30  21.4231548309
INFO:: Command: (rotamer-score 59 "A" 28 "")
   Rotamer 4 : m -30  21.4231548309
INFO:: Command: (turn-on-backup 59)
ok
test42_0 (__main__.PdbMtzTestFunctions)
Align and mutate a model with deletions ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb
 PDB file /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 50/87
Molecule 60 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: aligning to mol number 60 chain: A

----- input to align_on_chain() -----------------
        chain A
        target DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
        wgap  -0.5
        is_nucleic_acid_flag 0
        console_output 1
---------------------------------------------------
INFO:: input model  sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID
INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
>  /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb
---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID
> target seq: 
DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
INFO:: alignment score 163.5
DEBUG:: s.length() 95
DEBUG:: nSelResidues 87
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Tue_Dec_27_04:14:17_2016_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: 616279952 "A" 1 ""] -> ASP
      [spec: 616279952 "A" 2 ""] -> VAL
      [spec: 616279952 "A" 3 ""] -> SER
      [spec: 616279952 "A" 11 ""] -> LEU
      [spec: 616279952 "A" 12 ""] -> PRO
      [spec: 616279952 "A" 13 ""] -> PRO
      [spec: 616279952 "A" 62 ""] -> PRO
      [spec: 616279952 "A" 63 ""] -> GLY
   Deletions:
      [spec: 616279952 "A" 24 ""]
      [spec: 616279952 "A" 33 ""]
   Mutations:
apply resno updates... 
Applied 3 insertions 
Applied 0 mutations 
Applied 2 deletions 
INFO:: Command: (write-pdb-file 60 "mutated.pdb")
    ::::: [60, 'A', 1, ''] False False
    ::::: [60, 'A', 4, ''] True True
    ::::: [60, 'A', 59, ''] True True
    ::::: [60, 'A', 60, ''] False False
    ::::: [60, 'A', 61, ''] False False
    ::::: [60, 'A', 93, ''] True True
    ::::: [60, 'A', 94, ''] False False
ok
test42_1 (__main__.PdbMtzTestFunctions)
Renumber residues should be in seqnum order ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 61 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:18_2016_modification_0.pdb.gz
INFO:: Command: (renumber-residue-range 61 "A" 10 20 100)
INFO:: Command: (setnum-from-serial-number 61 "A" 90)
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 62 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:19_2016_modification_0.pdb.gz
INFO:: Command: (renumber-residue-range 62 "A" 10 20 -100)
INFO:: Command: (setnum-from-serial-number 62 "A" 0)
ok
test43_0 (__main__.PdbMtzTestFunctions)
Autofit Rotamer on Residue with Insertion codes ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb3hfl.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb3hfl.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb3hfl.ent has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: NCS chain comparison 15/212
INFO:: NCS chain comparison 7/212
INFO:: NCS chain comparison 10/215
Molecule 63 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz
Number of OBSERVED reflections: 17920
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = (  64,  96,  90)
INFO:: 0.045 seconds to read MTZ file
INFO:: 0.009 seconds to initialize map
INFO:: 0.019 seconds for FFT
INFO:: 0.005 seconds for statistics
      Map mean: ........ 2.00384e-11
      Map sigma: ....... 0.260405
      Map maximum: ..... 1.71787
      Map minimum: ..... -1.03389
INFO:: 0.012 seconds for contour map
INFO:: 0.09 seconds in total
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Tue_Dec_27_04:14:19_2016_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Fitting score for best rotamer: 5.83405
INFO:: Command: (auto-fit-best-rotamer 52 "" "A" "H" 63 64 0  0.00)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Tue_Dec_27_04:14:19_2016_modification_1.pdb.gz
ok
test44_0 (__main__.PdbMtzTestFunctions)
RNA base has correct residue type after mutation ... INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.0120681
    rms devi: 0.0134464
    max devi: 0.0214179
    min devi: 0.00385596
INFO:: 5 matched atoms had: 
   mean devi: 0.270216
    rms devi: 0.335002
    max devi: 0.536002
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.26738
    rms devi: 0.322791
    max devi: 0.495136
    min devi: 0.112289
INFO:: 5 matched atoms had: 
   mean devi: 0.270247
    rms devi: 0.335033
    max devi: 0.536044
    min devi: 0.0847029
INFO:: 5 matched atoms had: 
   mean devi: 0.267411
    rms devi: 0.322823
    max devi: 0.495177
    min devi: 0.112221
INFO:: 5 matched atoms had: 
   mean devi: 0.011982
    rms devi: 0.013349
    max devi: 0.0212578
    min devi: 0.0038732
INFO:: 5 matched atoms had: 
   mean devi: 0.000242576
    rms devi: 0.000242751
    max devi: 0.000256671
    min devi: 0.000231275
INFO:: 5 matched atoms had: 
   mean devi: 0.270185
    rms devi: 0.334971
    max devi: 0.535961
    min devi: 0.0845571
INFO:: 5 matched atoms had: 
   mean devi: 0.267349
    rms devi: 0.322759
    max devi: 0.495094
    min devi: 0.112357
INFO:: 5 matched atoms had: 
   mean devi: 6.9313e-05
    rms devi: 6.93629e-05
    max devi: 7.33402e-05
    min devi: 6.60841e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.0120334
    rms devi: 0.0134072
    max devi: 0.0213538
    min devi: 0.00386188
INFO:: 5 matched atoms had: 
   mean devi: 0.000138622
    rms devi: 0.000138721
    max devi: 0.000146676
    min devi: 0.000132164
INFO:: 5 matched atoms had: 
   mean devi: 0.011999
    rms devi: 0.0133684
    max devi: 0.0212898
    min devi: 0.0038691
INFO:: 5 matched atoms had: 
   mean devi: 0.267426
    rms devi: 0.322839
    max devi: 0.495197
    min devi: 0.112187
INFO:: 5 matched atoms had: 
   mean devi: 0.270294
    rms devi: 0.335079
    max devi: 0.536106
    min devi: 0.0848122
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Dec_27_04:14:19_2016_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")
INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Dec_27_04:14:19_2016_modification_1.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.269035
    rms devi: 0.337196
    max devi: 0.547544
    min devi: 0.0817551
INFO:: Command: (mutate-base 65 "A" 2 "" "C")
  mutated base to type C - was A
INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.0120681
    rms devi: 0.0134464
    max devi: 0.0214179
    min devi: 0.00385596
INFO:: 5 matched atoms had: 
   mean devi: 0.270216
    rms devi: 0.335002
    max devi: 0.536002
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.26738
    rms devi: 0.322791
    max devi: 0.495136
    min devi: 0.112289
INFO:: 5 matched atoms had: 
   mean devi: 0.270247
    rms devi: 0.335033
    max devi: 0.536044
    min devi: 0.0847029
INFO:: 5 matched atoms had: 
   mean devi: 0.267411
    rms devi: 0.322823
    max devi: 0.495177
    min devi: 0.112221
INFO:: 5 matched atoms had: 
   mean devi: 0.011982
    rms devi: 0.013349
    max devi: 0.0212578
    min devi: 0.0038732
INFO:: 5 matched atoms had: 
   mean devi: 0.000242576
    rms devi: 0.000242751
    max devi: 0.000256671
    min devi: 0.000231275
INFO:: 5 matched atoms had: 
   mean devi: 0.270185
    rms devi: 0.334971
    max devi: 0.535961
    min devi: 0.0845571
INFO:: 5 matched atoms had: 
   mean devi: 0.267349
    rms devi: 0.322759
    max devi: 0.495094
    min devi: 0.112357
INFO:: 5 matched atoms had: 
   mean devi: 6.9313e-05
    rms devi: 6.93629e-05
    max devi: 7.33402e-05
    min devi: 6.60841e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.0120334
    rms devi: 0.0134072
    max devi: 0.0213538
    min devi: 0.00386188
INFO:: 5 matched atoms had: 
   mean devi: 0.000138622
    rms devi: 0.000138721
    max devi: 0.000146676
    min devi: 0.000132164
INFO:: 5 matched atoms had: 
   mean devi: 0.011999
    rms devi: 0.0133684
    max devi: 0.0212898
    min devi: 0.0038691
INFO:: 5 matched atoms had: 
   mean devi: 0.267426
    rms devi: 0.322839
    max devi: 0.495197
    min devi: 0.112187
INFO:: 5 matched atoms had: 
   mean devi: 0.270294
    rms devi: 0.335079
    max devi: 0.536106
    min devi: 0.0848122
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Dec_27_04:14:19_2016_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")
INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Dec_27_04:14:19_2016_modification_1.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.269035
    rms devi: 0.337196
    max devi: 0.547544
    min devi: 0.0817551
INFO:: Command: (mutate-base 66 "A" 2 "" "Cr")
  mutated base to type Cr - was A
ok
test45_0 (__main__.PdbMtzTestFunctions)
DNA bases are the correct residue type after mutation ... INFO:: 5 matched atoms had: 
   mean devi: 0.00589883
    rms devi: 0.00670957
    max devi: 0.0101325
    min devi: 0.00258111
INFO:: 5 matched atoms had: 
   mean devi: 0.00725623
    rms devi: 0.00778801
    max devi: 0.0125644
    min devi: 0.00456024
INFO:: 5 matched atoms had: 
   mean devi: 0.271793
    rms devi: 0.336384
    max devi: 0.533839
    min devi: 0.0878288
INFO:: 5 matched atoms had: 
   mean devi: 0.26776
    rms devi: 0.326512
    max devi: 0.505569
    min devi: 0.10459
INFO:: 5 matched atoms had: 
   mean devi: 0.271823
    rms devi: 0.336416
    max devi: 0.53388
    min devi: 0.0879009
INFO:: 5 matched atoms had: 
   mean devi: 0.267791
    rms devi: 0.326544
    max devi: 0.505617
    min devi: 0.104522
INFO:: 5 matched atoms had: 
   mean devi: 0.00717866
    rms devi: 0.00770023
    max devi: 0.0124098
    min devi: 0.00457508
INFO:: 5 matched atoms had: 
   mean devi: 0.00574436
    rms devi: 0.00657052
    max devi: 0.0099594
    min devi: 0.0024248
INFO:: 5 matched atoms had: 
   mean devi: 0.271762
    rms devi: 0.336353
    max devi: 0.533797
    min devi: 0.0877567
INFO:: 5 matched atoms had: 
   mean devi: 0.267729
    rms devi: 0.326479
    max devi: 0.505521
    min devi: 0.104657
INFO:: 5 matched atoms had: 
   mean devi: 0.00585391
    rms devi: 0.00666923
    max devi: 0.0100827
    min devi: 0.00253528
INFO:: 5 matched atoms had: 
   mean devi: 0.00722485
    rms devi: 0.00775255
    max devi: 0.0125025
    min devi: 0.00456535
INFO:: 5 matched atoms had: 
   mean devi: 0.00580961
    rms devi: 0.00662938
    max devi: 0.0100332
    min devi: 0.00249036
INFO:: 5 matched atoms had: 
   mean devi: 0.00719394
    rms devi: 0.00771755
    max devi: 0.0124407
    min devi: 0.00457156
INFO:: 5 matched atoms had: 
   mean devi: 0.267807
    rms devi: 0.326561
    max devi: 0.505641
    min devi: 0.104488
INFO:: 5 matched atoms had: 
   mean devi: 0.27187
    rms devi: 0.336463
    max devi: 0.533942
    min devi: 0.088009
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG")
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_1.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.270191
    rms devi: 0.336363
    max devi: 0.538427
    min devi: 0.0854029
INFO:: Command: (mutate-base 67 "A" 2 "" "DC")
  mutated base to type DC
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_2.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.271895
    rms devi: 0.336278
    max devi: 0.534478
    min devi: 0.0923473
INFO:: Command: (mutate-base 67 "A" 2 "" "DG")
  mutated base to type DG
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_3.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.0043292
    rms devi: 0.00481764
    max devi: 0.00738267
    min devi: 0.00186162
INFO:: Command: (mutate-base 67 "A" 2 "" "DA")
  mutated base to type DA
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_4.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.265718
    rms devi: 0.326008
    max devi: 0.501859
    min devi: 0.0926641
INFO:: Command: (mutate-base 67 "A" 2 "" "DT")
  mutated base to type DT
INFO:: 5 matched atoms had: 
   mean devi: 0.00589883
    rms devi: 0.00670957
    max devi: 0.0101325
    min devi: 0.00258111
INFO:: 5 matched atoms had: 
   mean devi: 0.00725623
    rms devi: 0.00778801
    max devi: 0.0125644
    min devi: 0.00456024
INFO:: 5 matched atoms had: 
   mean devi: 0.271793
    rms devi: 0.336384
    max devi: 0.533839
    min devi: 0.0878288
INFO:: 5 matched atoms had: 
   mean devi: 0.26776
    rms devi: 0.326512
    max devi: 0.505569
    min devi: 0.10459
INFO:: 5 matched atoms had: 
   mean devi: 0.271823
    rms devi: 0.336416
    max devi: 0.53388
    min devi: 0.0879009
INFO:: 5 matched atoms had: 
   mean devi: 0.267791
    rms devi: 0.326544
    max devi: 0.505617
    min devi: 0.104522
INFO:: 5 matched atoms had: 
   mean devi: 0.00717866
    rms devi: 0.00770023
    max devi: 0.0124098
    min devi: 0.00457508
INFO:: 5 matched atoms had: 
   mean devi: 0.00574436
    rms devi: 0.00657052
    max devi: 0.0099594
    min devi: 0.0024248
INFO:: 5 matched atoms had: 
   mean devi: 0.271762
    rms devi: 0.336353
    max devi: 0.533797
    min devi: 0.0877567
INFO:: 5 matched atoms had: 
   mean devi: 0.267729
    rms devi: 0.326479
    max devi: 0.505521
    min devi: 0.104657
INFO:: 5 matched atoms had: 
   mean devi: 0.00585391
    rms devi: 0.00666923
    max devi: 0.0100827
    min devi: 0.00253528
INFO:: 5 matched atoms had: 
   mean devi: 0.00722485
    rms devi: 0.00775255
    max devi: 0.0125025
    min devi: 0.00456535
INFO:: 5 matched atoms had: 
   mean devi: 0.00580961
    rms devi: 0.00662938
    max devi: 0.0100332
    min devi: 0.00249036
INFO:: 5 matched atoms had: 
   mean devi: 0.00719394
    rms devi: 0.00771755
    max devi: 0.0124407
    min devi: 0.00457156
INFO:: 5 matched atoms had: 
   mean devi: 0.267807
    rms devi: 0.326561
    max devi: 0.505641
    min devi: 0.104488
INFO:: 5 matched atoms had: 
   mean devi: 0.27187
    rms devi: 0.336463
    max devi: 0.533942
    min devi: 0.088009
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG")
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_1.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.270191
    rms devi: 0.336363
    max devi: 0.538427
    min devi: 0.0854029
INFO:: Command: (mutate-base 68 "A" 2 "" "Cd")
  mutated base to type Cd
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_2.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.271895
    rms devi: 0.336278
    max devi: 0.534478
    min devi: 0.0923473
INFO:: Command: (mutate-base 68 "A" 2 "" "Gd")
  mutated base to type Gd
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_3.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.0043292
    rms devi: 0.00481764
    max devi: 0.00738267
    min devi: 0.00186162
INFO:: Command: (mutate-base 68 "A" 2 "" "Ad")
  mutated base to type Ad
INFO:: backup file coot-backup/Ideal-A-form-DNA_Tue_Dec_27_04:14:20_2016_modification_4.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0.265718
    rms devi: 0.326008
    max devi: 0.501859
    min devi: 0.0926641
INFO:: Command: (mutate-base 68 "A" 2 "" "Td")
  mutated base to type Td
ok
test46_0 (__main__.PdbMtzTestFunctions)
SegIDs are correct after mutate ... Symmetry available for this molecule
INFO:: Command: (copy-molecule 0)
INFO:: mutate 32 A to a LYS
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:20_2016_modification_0.pdb.gz
INFO:: Command: (mutate 69 "A" 32 "" "LYS")
ok
test47_0 (__main__.PdbMtzTestFunctions)
TER on water chain is removed on adding a water by hand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb
 PDB file /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 70 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (set-rotation-centre  3.00  4.00  5.00)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_some-waters-with-ter.pdb_Tue_Dec_27_04:14:20_2016_modification_0.pdb.gz
1/D/79 {HOH}/ O   altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (write-pdb-file 70 "tmp-with-new-water.pdb")
ok
test48_0 (__main__.PdbMtzTestFunctions)
TER on water chain is removed on adding waters automatically ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tm+some-waters.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 71 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 0.2
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.311501
INFO:: Using density cut-off: 0.0623002 (0.2 sigma)  (mean -0.0338336 stdev: 0.14627)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
-------------------------------------------------------------
INFO:: cluster at xyz = (     27.82,     31.44,     8.887) is too big to be water
INFO:: cluster at xyz = (     70.04,      19.1,     18.63) is too big to be water
INFO:: cluster at xyz = (     69.25,     5.345,     11.11) is too big to be water
INFO:: cluster at xyz = (     52.69,     10.79,     11.51) is too big to be water
INFO:: cluster at xyz = (     72.02,     12.27,     14.68) is too big to be water
INFO:: cluster at xyz = (     39.69,     8.165,     19.55) is too big to be water
INFO:: cluster at xyz = (      53.3,    -4.968,    -2.722) is too big to be water
INFO:: cluster at xyz = (     40.99,     7.049,     16.27) is too big to be water
INFO:: cluster at xyz = (     25.71,     4.246,     5.745) is too big to be water
INFO:: found 46 waters in water fitting
Done - back from lig.water_fit()
DEBUG::  new_waters_mol_flag: 0
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tm+some-waters.pdb_Tue_Dec_27_04:14:21_2016_modification_0.pdb.gz
INFO:: Adding to solvent chain: D
INFO:: Command: (write-pdb-file 71 "auto-waters.pdb")
ok
test48_1 (__main__.PdbMtzTestFunctions)
Adding atoms to Many-Chained Molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 72 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_0.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_1.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_2.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_3.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_4.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_5.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_6.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_7.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_8.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_9.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_10.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_11.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_12.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_13.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_14.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_15.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_16.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_17.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_18.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_19.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_20.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_21.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_22.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_23.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_24.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_25.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_26.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_27.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_28.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_29.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_30.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_31.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_32.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_33.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_34.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_35.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_36.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_37.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_38.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_39.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_40.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_41.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_42.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_43.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_44.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_45.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_46.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_47.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_48.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_49.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_50.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_51.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_52.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_53.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_54.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_55.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_56.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_57.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_58.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_59.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_60.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_61.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_62.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_63.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_64.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_65.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_66.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_67.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_68.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_69.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_70.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_71.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_72.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_73.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_74.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_75.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_76.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_77.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_78.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_79.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_80.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_81.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_82.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_83.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_84.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_85.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_86.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_87.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_88.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_89.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_90.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_91.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_92.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_93.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_94.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_95.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_96.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_97.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_98.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:22_2016_modification_99.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Mg")
ok
test49_0 (__main__.PdbMtzTestFunctions)
Arrange waters round protein ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb
 PDB file /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 73 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_water-test-no-cell.pdb_Tue_Dec_27_04:14:26_2016_modification_0.pdb.gz
No symmetry available
INFO:: moved 0 water molecules
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pathological-water-test.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb
 PDB file /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 74 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pathological-water-test.pdb_Tue_Dec_27_04:14:26_2016_modification_0.pdb.gz
INFO:: moved 181 water molecules
INFO:: Command: (write-pdb-file 74 "waters-moved-failure.pdb")
ok
test50_0 (__main__.PdbMtzTestFunctions)
Correct Segid After Add Terminal Residue ... Symmetry available for this molecule
INFO:: Command: (copy-molecule 0)
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.05 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.027 seconds for FFT
INFO:: 0.005 seconds for statistics
      Map mean: ........ 1.06932e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.026 seconds for contour map
INFO:: 0.109 seconds in total
INFO:: Masking around 58 atoms
fitting terminal residue with 1000 random trials
--- in best_fit_phi_psi() with offset 1
INFO:: Fitting terminal residue  without individual rigid body fitting.
--- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000
                     called fit_terminal_residue_generic() residue-seqnum: 93 offset: 1
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:27_2016_modification_0.pdb.gz
INFO:: Command: (add-terminal-residue 75 "A" 93 1)
ok
test51_0 (__main__.PdbMtzTestFunctions)
Correct Segid after NCS residue range copy ... Symmetry available for this molecule
INFO:: Command: (copy-molecule 0)
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 77 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 77 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: (44.878,12.955,8.761) B-factor: 30.17
First atom of 745 in second selection 1/B/1 {ASP}/ N   altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03
INFO:: LSQ matched 93 atoms
INFO:: 93 matched atoms had: 
   mean devi: 1.17877
    rms devi: 4.85919
    max devi: 46.259
    min devi: 0.125386
   find_ncs_matrix returns (LSQ) 
|    0.9637,  -0.07462,   -0.2563|
|    0.2651,    0.3804,     0.886|
|    0.0314,   -0.9218,    0.3864|
(     38.09,    -17.87,     14.32)
   Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
   Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:27_2016_modification_0.pdb.gz
ok
test52_0 (__main__.PdbMtzTestFunctions)
Merge Water Chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 78 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (turn-off-backup 78)
0//-32767 {HOH}/ O   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain)
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 43.60  8.69 12.91)
1/C/2 {HOH}/ O   altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 45.60  8.69 12.91)
1/C/3 {HOH}/ O   altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 47.60  8.69 12.91)
1/C/4 {HOH}/ O   altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 49.60  8.69 12.91)
1/C/5 {HOH}/ O   altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 51.60  8.69 12.91)
INFO:: Command: (renumber-residue-range 78 "D" 1 5 10)
1/D/16 {HOH}/ O   altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 53.60  8.69 12.91)
1/D/17 {HOH}/ O   altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 55.60  8.69 12.91)
1/D/18 {HOH}/ O   altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 57.60  8.69 12.91)
1/D/19 {HOH}/ O   altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 59.60  8.69 12.91)
1/D/20 {HOH}/ O   altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 61.60  8.69 12.91)
INFO:: Command: (renumber-residue-range 78 "E" 11 15 5)
1/D/21 {HOH}/ O   altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 63.60  8.69 12.91)
1/D/22 {HOH}/ O   altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 65.60  8.69 12.91)
1/D/23 {HOH}/ O   altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 67.60  8.69 12.91)
1/D/24 {HOH}/ O   altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 69.60  8.69 12.91)
1/D/25 {HOH}/ O   altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 71.60  8.69 12.91)
INFO:: Command: (renumber-residue-range 78 "F" 16 20 2)
INFO:: Command: (n-chains 78)
INFO:: Command: (chain_id 78 0)
INFO:: Command: (chain_id 78 1)
INFO:: Command: (chain_id 78 2)
INFO:: Command: (chain_id 78 3)
INFO:: Command: (chain_id 78 4)
INFO:: Command: (is-solvent-chain-p 78 "A")
INFO:: Command: (is-solvent-chain-p 78 "B")
INFO:: Command: (is-solvent-chain-p 78 "D")
INFO:: Command: (is-solvent-chain-p 78 "E")
INFO:: Command: (is-solvent-chain-p 78 "F")
INFO:: Command: (renumber-residue-range 78 "E" 1 5 5)
INFO:: Command: (renumber-residue-range 78 "F" 1 5 10)
INFO:: Command: (turn-on-backup 78)
INFO:: Command: (n-chains 78)
INFO:: Command: (chain_id 78 2)
INFO:: Command: (setnum-from-serial-number 78 "D" 0)
INFO:: Command: (setnum-from-serial-number 78 "D" 14)
ok
test52_1 (__main__.PdbMtzTestFunctions)
Consolidated merge ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 79 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 80 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 81 read successfully
DEBUG:: there were 1 types with no dictionary 
-------- starting chain list -----------
INFO:: Command: (n-chains 79)
INFO:: Command: (chain_id 79 0)
INFO:: Command: (chain_id 79 1)
INFO:: Command: (chain_id 79 2)
INFO:: Command: (chain_id 79 3)
INFO:: Command: (chain_id 79 4)
['A', 'B', 'C', 'D', '']
-X,-X+Y,-Z+1/3 ->
-1 0 0
-1 1 0
0 0 -1
translations: 0 0 0.333333
pre-trans: 0 0 0
Symmetry available for this molecule
INFO:: Command: (update-go-to-atom-window-on-new-mol)
INFO:: Command: (n-chains 79)
INFO:: Command: (chain_id 79 0)
INFO:: Command: (chain_id 79 1)
INFO:: Command: (chain_id 79 2)
INFO:: Command: (chain_id 79 3)
INFO:: Command: (chain_id 79 4)
INFO:: Command: (chain_id 79 5)
INFO:: Command: (chain_id 79 6)
INFO:: Command: (chain_id 79 7)
INFO:: Command: (chain_id 79 8)
INFO:: Command: (chain_id 79 9)
INFO:: Command: (chain_id 79 10)
INFO:: Command: (chain_id 79 11)
['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K']
INFO:: Command: (write-pdb-file 79 "sym-merged.pdb")
ok
test53_0 (__main__.PdbMtzTestFunctions)
LSQ by atom ... Symmetry available for this molecule
INFO:: Command: (copy-molecule 0)
Symmetry available for this molecule
INFO:: Command: (copy-molecule 0)
INFO:: Matching/moving molecule number 84 to 83
INFO:: LSQ matched 4 atoms
INFO:: 4 matched atoms had: 
   mean devi: 0.0353197
    rms devi: 0.0377881
    max devi: 0.0545286
    min devi: 0.016676
INFO:: Axis orientation: (    0.9786,    0.1755,   -0.1076)
INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:30_2016_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)
ok
test53_1 (__main__.PdbMtzTestFunctions)
LSQing changes the space-group and cell to that of the reference molecule ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 85 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1py3.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1py3.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1py3.ent has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 91/204
INFO:: NCS chain comparison 90/204
INFO:: NCS chain comparison 175/179
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain B"
Molecule 86 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 85 to 86
INFO:: LSQ matched 164 atoms
INFO:: 164 matched atoms had: 
   mean devi: 0.502333
    rms devi: 0.593803
    max devi: 1.67852
    min devi: 0.0431788
INFO:: Axis orientation: (     0.567,   -0.7175,    0.4046)
INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:31_2016_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
ok
test53_2 (__main__.PdbMtzTestFunctions)
set_residue_name sets the correct residue ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 87 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:32_2016_modification_0.pdb.gz
INFO:: Command: (set-residue-name 87 "A" 37 "" "FRE")
INFO:: Command: (n-chains 87)
INFO:: Command: (chain_id 87 0)
INFO:: Command: (chain_id 87 1)
INFO:: Command: (setnum-from-serial-number 87 "A" 0)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 0)
INFO:: Command: (setnum-from-serial-number 87 "A" 1)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 1)
INFO:: Command: (setnum-from-serial-number 87 "A" 2)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 2)
INFO:: Command: (setnum-from-serial-number 87 "A" 3)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 3)
INFO:: Command: (setnum-from-serial-number 87 "A" 4)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 4)
INFO:: Command: (setnum-from-serial-number 87 "A" 5)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 5)
INFO:: Command: (setnum-from-serial-number 87 "A" 6)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 6)
INFO:: Command: (setnum-from-serial-number 87 "A" 7)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 7)
INFO:: Command: (setnum-from-serial-number 87 "A" 8)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 8)
INFO:: Command: (setnum-from-serial-number 87 "A" 9)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 9)
INFO:: Command: (setnum-from-serial-number 87 "A" 10)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 10)
INFO:: Command: (setnum-from-serial-number 87 "A" 11)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 11)
INFO:: Command: (setnum-from-serial-number 87 "A" 12)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 12)
INFO:: Command: (setnum-from-serial-number 87 "A" 13)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 13)
INFO:: Command: (setnum-from-serial-number 87 "A" 14)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 14)
INFO:: Command: (setnum-from-serial-number 87 "A" 15)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 15)
INFO:: Command: (setnum-from-serial-number 87 "A" 16)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 16)
INFO:: Command: (setnum-from-serial-number 87 "A" 17)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 17)
INFO:: Command: (setnum-from-serial-number 87 "A" 18)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 18)
INFO:: Command: (setnum-from-serial-number 87 "A" 19)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 19)
INFO:: Command: (setnum-from-serial-number 87 "A" 20)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 20)
INFO:: Command: (setnum-from-serial-number 87 "A" 21)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 21)
INFO:: Command: (setnum-from-serial-number 87 "A" 22)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 22)
INFO:: Command: (setnum-from-serial-number 87 "A" 23)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 23)
INFO:: Command: (setnum-from-serial-number 87 "A" 24)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 24)
INFO:: Command: (setnum-from-serial-number 87 "A" 25)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 25)
INFO:: Command: (setnum-from-serial-number 87 "A" 26)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 26)
INFO:: Command: (setnum-from-serial-number 87 "A" 27)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 27)
INFO:: Command: (setnum-from-serial-number 87 "A" 28)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 28)
INFO:: Command: (setnum-from-serial-number 87 "A" 29)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 29)
INFO:: Command: (setnum-from-serial-number 87 "A" 30)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 30)
INFO:: Command: (setnum-from-serial-number 87 "A" 31)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 31)
INFO:: Command: (setnum-from-serial-number 87 "A" 32)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 32)
INFO:: Command: (setnum-from-serial-number 87 "A" 33)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 33)
INFO:: Command: (setnum-from-serial-number 87 "A" 34)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 34)
INFO:: Command: (setnum-from-serial-number 87 "A" 35)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 35)
INFO:: Command: (setnum-from-serial-number 87 "A" 36)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 36)
INFO:: Command: (setnum-from-serial-number 87 "A" 37)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 37)
INFO:: Command: (setnum-from-serial-number 87 "A" 38)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 38)
INFO:: Command: (setnum-from-serial-number 87 "A" 39)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 39)
INFO:: Command: (setnum-from-serial-number 87 "A" 40)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 40)
INFO:: Command: (setnum-from-serial-number 87 "A" 41)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 41)
INFO:: Command: (setnum-from-serial-number 87 "A" 42)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 42)
INFO:: Command: (setnum-from-serial-number 87 "A" 43)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 43)
INFO:: Command: (setnum-from-serial-number 87 "A" 44)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 44)
INFO:: Command: (setnum-from-serial-number 87 "A" 45)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 45)
INFO:: Command: (setnum-from-serial-number 87 "A" 46)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 46)
INFO:: Command: (setnum-from-serial-number 87 "A" 47)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 47)
INFO:: Command: (setnum-from-serial-number 87 "A" 48)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 48)
INFO:: Command: (setnum-from-serial-number 87 "A" 49)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 49)
INFO:: Command: (setnum-from-serial-number 87 "A" 50)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 50)
INFO:: Command: (setnum-from-serial-number 87 "A" 51)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 51)
INFO:: Command: (setnum-from-serial-number 87 "A" 52)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 52)
INFO:: Command: (setnum-from-serial-number 87 "A" 53)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 53)
INFO:: Command: (setnum-from-serial-number 87 "A" 54)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 54)
INFO:: Command: (setnum-from-serial-number 87 "A" 55)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 55)
INFO:: Command: (setnum-from-serial-number 87 "A" 56)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 56)
INFO:: Command: (setnum-from-serial-number 87 "A" 57)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 57)
INFO:: Command: (setnum-from-serial-number 87 "A" 58)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 58)
INFO:: Command: (setnum-from-serial-number 87 "A" 59)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 59)
INFO:: Command: (setnum-from-serial-number 87 "A" 60)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 60)
INFO:: Command: (setnum-from-serial-number 87 "A" 61)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 61)
INFO:: Command: (setnum-from-serial-number 87 "A" 62)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 62)
INFO:: Command: (setnum-from-serial-number 87 "A" 63)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 63)
INFO:: Command: (setnum-from-serial-number 87 "A" 64)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 64)
INFO:: Command: (setnum-from-serial-number 87 "A" 65)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 65)
INFO:: Command: (setnum-from-serial-number 87 "A" 66)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 66)
INFO:: Command: (setnum-from-serial-number 87 "A" 67)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 67)
INFO:: Command: (setnum-from-serial-number 87 "A" 68)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 68)
INFO:: Command: (setnum-from-serial-number 87 "A" 69)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 69)
INFO:: Command: (setnum-from-serial-number 87 "A" 70)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 70)
INFO:: Command: (setnum-from-serial-number 87 "A" 71)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 71)
INFO:: Command: (setnum-from-serial-number 87 "A" 72)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 72)
INFO:: Command: (setnum-from-serial-number 87 "A" 73)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 73)
INFO:: Command: (setnum-from-serial-number 87 "A" 74)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 74)
INFO:: Command: (setnum-from-serial-number 87 "A" 75)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 75)
INFO:: Command: (setnum-from-serial-number 87 "A" 76)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 76)
INFO:: Command: (setnum-from-serial-number 87 "A" 77)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 77)
INFO:: Command: (setnum-from-serial-number 87 "A" 78)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 78)
INFO:: Command: (setnum-from-serial-number 87 "A" 79)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 79)
INFO:: Command: (setnum-from-serial-number 87 "A" 80)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 80)
INFO:: Command: (setnum-from-serial-number 87 "A" 81)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 81)
INFO:: Command: (setnum-from-serial-number 87 "A" 82)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 82)
INFO:: Command: (setnum-from-serial-number 87 "A" 83)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 83)
INFO:: Command: (setnum-from-serial-number 87 "A" 84)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 84)
INFO:: Command: (setnum-from-serial-number 87 "A" 85)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 85)
INFO:: Command: (setnum-from-serial-number 87 "A" 86)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 86)
INFO:: Command: (setnum-from-serial-number 87 "A" 87)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 87)
INFO:: Command: (setnum-from-serial-number 87 "A" 88)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 88)
INFO:: Command: (setnum-from-serial-number 87 "A" 89)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 89)
INFO:: Command: (setnum-from-serial-number 87 "A" 90)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 90)
INFO:: Command: (setnum-from-serial-number 87 "A" 91)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 91)
INFO:: Command: (setnum-from-serial-number 87 "A" 92)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 92)
INFO:: Command: (setnum-from-serial-number 87 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 0)
INFO:: Command: (setnum-from-serial-number 87 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 1)
INFO:: Command: (setnum-from-serial-number 87 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 2)
INFO:: Command: (setnum-from-serial-number 87 "B" 3)
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INFO:: Command: (insertion-code-from-serial-number 87 "A" 90)
INFO:: Command: (setnum-from-serial-number 87 "A" 91)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 91)
INFO:: Command: (setnum-from-serial-number 87 "A" 92)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 92)
INFO:: Command: (setnum-from-serial-number 87 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 0)
INFO:: Command: (setnum-from-serial-number 87 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 1)
INFO:: Command: (setnum-from-serial-number 87 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 2)
INFO:: Command: (setnum-from-serial-number 87 "B" 3)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 3)
INFO:: Command: (setnum-from-serial-number 87 "B" 4)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 4)
INFO:: Command: (setnum-from-serial-number 87 "B" 5)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 5)
INFO:: Command: (setnum-from-serial-number 87 "B" 6)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 6)
INFO:: Command: (setnum-from-serial-number 87 "B" 7)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 7)
INFO:: Command: (setnum-from-serial-number 87 "B" 8)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 8)
INFO:: Command: (setnum-from-serial-number 87 "B" 9)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 9)
INFO:: Command: (setnum-from-serial-number 87 "B" 10)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 10)
INFO:: Command: (setnum-from-serial-number 87 "B" 11)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 11)
INFO:: Command: (setnum-from-serial-number 87 "B" 12)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 12)
INFO:: Command: (setnum-from-serial-number 87 "B" 13)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 13)
INFO:: Command: (setnum-from-serial-number 87 "B" 14)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 14)
INFO:: Command: (setnum-from-serial-number 87 "B" 15)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 15)
INFO:: Command: (setnum-from-serial-number 87 "B" 16)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 16)
INFO:: Command: (setnum-from-serial-number 87 "B" 17)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 17)
INFO:: Command: (setnum-from-serial-number 87 "B" 18)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 18)
INFO:: Command: (setnum-from-serial-number 87 "B" 19)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 19)
INFO:: Command: (setnum-from-serial-number 87 "B" 20)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 20)
INFO:: Command: (setnum-from-serial-number 87 "B" 21)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 21)
INFO:: Command: (setnum-from-serial-number 87 "B" 22)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 22)
INFO:: Command: (setnum-from-serial-number 87 "B" 23)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 23)
INFO:: Command: (setnum-from-serial-number 87 "B" 24)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 24)
INFO:: Command: (setnum-from-serial-number 87 "B" 25)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 25)
INFO:: Command: (setnum-from-serial-number 87 "B" 26)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 26)
INFO:: Command: (setnum-from-serial-number 87 "B" 27)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 27)
INFO:: Command: (setnum-from-serial-number 87 "B" 28)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 28)
INFO:: Command: (setnum-from-serial-number 87 "B" 29)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 29)
INFO:: Command: (setnum-from-serial-number 87 "B" 30)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 30)
INFO:: Command: (setnum-from-serial-number 87 "B" 31)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 31)
INFO:: Command: (setnum-from-serial-number 87 "B" 32)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 32)
INFO:: Command: (setnum-from-serial-number 87 "B" 33)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 33)
INFO:: Command: (setnum-from-serial-number 87 "B" 34)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 34)
INFO:: Command: (setnum-from-serial-number 87 "B" 35)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 35)
INFO:: Command: (setnum-from-serial-number 87 "B" 36)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 36)
INFO:: Command: (setnum-from-serial-number 87 "B" 37)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 37)
INFO:: Command: (setnum-from-serial-number 87 "B" 38)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 38)
INFO:: Command: (setnum-from-serial-number 87 "B" 39)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 39)
INFO:: Command: (setnum-from-serial-number 87 "B" 40)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 40)
INFO:: Command: (setnum-from-serial-number 87 "B" 41)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 41)
INFO:: Command: (setnum-from-serial-number 87 "B" 42)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 42)
INFO:: Command: (setnum-from-serial-number 87 "B" 43)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 43)
INFO:: Command: (setnum-from-serial-number 87 "B" 44)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 44)
INFO:: Command: (setnum-from-serial-number 87 "B" 45)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 45)
INFO:: Command: (setnum-from-serial-number 87 "B" 46)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 46)
INFO:: Command: (setnum-from-serial-number 87 "B" 47)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 47)
INFO:: Command: (setnum-from-serial-number 87 "B" 48)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 48)
INFO:: Command: (setnum-from-serial-number 87 "B" 49)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 49)
INFO:: Command: (setnum-from-serial-number 87 "B" 50)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 50)
INFO:: Command: (setnum-from-serial-number 87 "B" 51)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 51)
INFO:: Command: (setnum-from-serial-number 87 "B" 52)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 52)
INFO:: Command: (setnum-from-serial-number 87 "B" 53)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 53)
INFO:: Command: (setnum-from-serial-number 87 "B" 54)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 54)
INFO:: Command: (setnum-from-serial-number 87 "B" 55)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 55)
INFO:: Command: (setnum-from-serial-number 87 "B" 56)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 56)
INFO:: Command: (setnum-from-serial-number 87 "B" 57)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 57)
INFO:: Command: (setnum-from-serial-number 87 "B" 58)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 58)
INFO:: Command: (setnum-from-serial-number 87 "B" 59)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 59)
INFO:: Command: (setnum-from-serial-number 87 "B" 60)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 60)
INFO:: Command: (setnum-from-serial-number 87 "B" 61)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 61)
INFO:: Command: (setnum-from-serial-number 87 "B" 62)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 62)
INFO:: Command: (setnum-from-serial-number 87 "B" 63)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 63)
INFO:: Command: (setnum-from-serial-number 87 "B" 64)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 64)
INFO:: Command: (setnum-from-serial-number 87 "B" 65)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 65)
INFO:: Command: (setnum-from-serial-number 87 "B" 66)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 66)
INFO:: Command: (setnum-from-serial-number 87 "B" 67)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 67)
INFO:: Command: (setnum-from-serial-number 87 "B" 68)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 68)
INFO:: Command: (setnum-from-serial-number 87 "B" 69)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 69)
INFO:: Command: (setnum-from-serial-number 87 "B" 70)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 70)
INFO:: Command: (setnum-from-serial-number 87 "B" 71)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 71)
INFO:: Command: (setnum-from-serial-number 87 "B" 72)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 72)
INFO:: Command: (setnum-from-serial-number 87 "B" 73)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 73)
INFO:: Command: (setnum-from-serial-number 87 "B" 74)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 74)
INFO:: Command: (setnum-from-serial-number 87 "B" 75)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 75)
INFO:: Command: (setnum-from-serial-number 87 "B" 76)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 76)
INFO:: Command: (setnum-from-serial-number 87 "B" 77)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 77)
INFO:: Command: (setnum-from-serial-number 87 "B" 78)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 78)
INFO:: Command: (setnum-from-serial-number 87 "B" 79)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 79)
INFO:: Command: (setnum-from-serial-number 87 "B" 80)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 80)
INFO:: Command: (setnum-from-serial-number 87 "B" 81)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 81)
INFO:: Command: (setnum-from-serial-number 87 "B" 82)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 82)
INFO:: Command: (setnum-from-serial-number 87 "B" 83)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 83)
INFO:: Command: (setnum-from-serial-number 87 "B" 84)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 84)
INFO:: Command: (setnum-from-serial-number 87 "B" 85)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 85)
INFO:: Command: (setnum-from-serial-number 87 "B" 86)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 86)
INFO:: Command: (setnum-from-serial-number 87 "B" 87)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 87)
INFO:: Command: (setnum-from-serial-number 87 "B" 88)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 88)
INFO:: Command: (setnum-from-serial-number 87 "B" 89)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 89)
INFO:: Command: (setnum-from-serial-number 87 "B" 90)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 90)
INFO:: Command: (setnum-from-serial-number 87 "B" 91)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 91)
INFO:: Command: (setnum-from-serial-number 87 "B" 92)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 92)
INFO:: Command: (setnum-from-serial-number 87 "B" 93)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 93)
INFO:: Command: (setnum-from-serial-number 87 "B" 94)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 94)
INFO:: Command: (setnum-from-serial-number 87 "B" 95)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 95)
0 [87, 'A', 1, '']
1 [87, 'A', 2, '']
2 [87, 'A', 3, '']
3 [87, 'A', 4, '']
4 [87, 'A', 5, '']
5 [87, 'A', 6, '']
6 [87, 'A', 7, '']
7 [87, 'A', 8, '']
8 [87, 'A', 9, '']
9 [87, 'A', 10, '']
10 [87, 'A', 11, '']
11 [87, 'A', 12, '']
12 [87, 'A', 13, '']
13 [87, 'A', 14, '']
14 [87, 'A', 15, '']
15 [87, 'A', 16, '']
16 [87, 'A', 17, '']
17 [87, 'A', 18, '']
18 [87, 'A', 19, '']
19 [87, 'A', 20, '']
20 [87, 'A', 21, '']
21 [87, 'A', 22, '']
22 [87, 'A', 23, '']
23 [87, 'A', 24, '']
24 [87, 'A', 25, '']
25 [87, 'A', 26, '']
26 [87, 'A', 27, '']
27 [87, 'A', 28, '']
28 [87, 'A', 29, '']
29 [87, 'A', 30, '']
30 [87, 'A', 31, '']
31 [87, 'A', 32, '']
32 [87, 'A', 33, '']
33 [87, 'A', 34, '']
34 [87, 'A', 35, '']
35 [87, 'A', 36, '']
36 [87, 'A', 37, '']
36 [87, 'A', 37, '']
37 [87, 'A', 38, '']
38 [87, 'A', 39, '']
39 [87, 'A', 40, '']
40 [87, 'A', 41, '']
41 [87, 'A', 42, '']
42 [87, 'A', 43, '']
43 [87, 'A', 44, '']
44 [87, 'A', 45, '']
45 [87, 'A', 46, '']
46 [87, 'A', 47, '']
47 [87, 'A', 48, '']
48 [87, 'A', 49, '']
49 [87, 'A', 50, '']
50 [87, 'A', 51, '']
51 [87, 'A', 52, '']
52 [87, 'A', 53, '']
53 [87, 'A', 54, '']
54 [87, 'A', 55, '']
55 [87, 'A', 56, '']
56 [87, 'A', 57, '']
57 [87, 'A', 58, '']
58 [87, 'A', 59, '']
59 [87, 'A', 60, '']
60 [87, 'A', 61, '']
61 [87, 'A', 62, '']
62 [87, 'A', 63, '']
63 [87, 'A', 64, '']
64 [87, 'A', 65, '']
65 [87, 'A', 66, '']
66 [87, 'A', 67, '']
67 [87, 'A', 68, '']
68 [87, 'A', 69, '']
69 [87, 'A', 70, '']
70 [87, 'A', 71, '']
71 [87, 'A', 72, '']
72 [87, 'A', 73, '']
73 [87, 'A', 74, '']
74 [87, 'A', 75, '']
75 [87, 'A', 76, '']
76 [87, 'A', 77, '']
77 [87, 'A', 78, '']
78 [87, 'A', 79, '']
79 [87, 'A', 80, '']
80 [87, 'A', 81, '']
81 [87, 'A', 82, '']
82 [87, 'A', 83, '']
83 [87, 'A', 84, '']
84 [87, 'A', 85, '']
85 [87, 'A', 86, '']
86 [87, 'A', 87, '']
87 [87, 'A', 88, '']
88 [87, 'A', 89, '']
89 [87, 'A', 90, '']
90 [87, 'A', 91, '']
91 [87, 'A', 92, '']
92 [87, 'A', 93, '']
93 [87, 'B', 1, '']
94 [87, 'B', 2, '']
95 [87, 'B', 3, '']
96 [87, 'B', 4, '']
97 [87, 'B', 5, '']
98 [87, 'B', 6, '']
99 [87, 'B', 7, '']
100 [87, 'B', 8, '']
101 [87, 'B', 9, '']
102 [87, 'B', 10, '']
103 [87, 'B', 11, '']
104 [87, 'B', 12, '']
105 [87, 'B', 13, '']
106 [87, 'B', 14, '']
107 [87, 'B', 15, '']
108 [87, 'B', 16, '']
109 [87, 'B', 17, '']
110 [87, 'B', 18, '']
111 [87, 'B', 19, '']
112 [87, 'B', 20, '']
113 [87, 'B', 21, '']
114 [87, 'B', 22, '']
115 [87, 'B', 23, '']
116 [87, 'B', 24, '']
117 [87, 'B', 25, '']
118 [87, 'B', 26, '']
119 [87, 'B', 27, '']
120 [87, 'B', 28, '']
121 [87, 'B', 29, '']
122 [87, 'B', 30, '']
123 [87, 'B', 31, '']
124 [87, 'B', 32, '']
125 [87, 'B', 33, '']
126 [87, 'B', 34, '']
127 [87, 'B', 35, '']
128 [87, 'B', 36, '']
129 [87, 'B', 37, '']
130 [87, 'B', 38, '']
131 [87, 'B', 39, '']
132 [87, 'B', 40, '']
133 [87, 'B', 41, '']
134 [87, 'B', 42, '']
135 [87, 'B', 43, '']
136 [87, 'B', 44, '']
137 [87, 'B', 45, '']
138 [87, 'B', 46, '']
139 [87, 'B', 47, '']
140 [87, 'B', 48, '']
141 [87, 'B', 49, '']
142 [87, 'B', 50, '']
143 [87, 'B', 51, '']
144 [87, 'B', 52, '']
145 [87, 'B', 53, '']
146 [87, 'B', 54, '']
147 [87, 'B', 55, '']
148 [87, 'B', 56, '']
149 [87, 'B', 57, '']
150 [87, 'B', 58, '']
151 [87, 'B', 59, '']
152 [87, 'B', 60, '']
153 [87, 'B', 61, '']
154 [87, 'B', 62, '']
155 [87, 'B', 63, '']
156 [87, 'B', 64, '']
157 [87, 'B', 65, '']
158 [87, 'B', 66, '']
159 [87, 'B', 67, '']
160 [87, 'B', 68, '']
161 [87, 'B', 69, '']
162 [87, 'B', 70, '']
163 [87, 'B', 71, '']
164 [87, 'B', 72, '']
165 [87, 'B', 73, '']
166 [87, 'B', 74, '']
167 [87, 'B', 75, '']
168 [87, 'B', 76, '']
169 [87, 'B', 77, '']
170 [87, 'B', 78, '']
171 [87, 'B', 79, '']
172 [87, 'B', 80, '']
173 [87, 'B', 81, '']
174 [87, 'B', 82, '']
175 [87, 'B', 83, '']
176 [87, 'B', 84, '']
177 [87, 'B', 85, '']
178 [87, 'B', 86, '']
179 [87, 'B', 87, '']
180 [87, 'B', 88, '']
181 [87, 'B', 89, '']
182 [87, 'B', 90, '']
183 [87, 'B', 91, '']
184 [87, 'B', 92, '']
185 [87, 'B', 93, '']
186 [87, 'B', 94, '']
187 [87, 'B', 95, '']
188 [87, 'B', 96, '']
ok
test53_3 (__main__.PdbMtzTestFunctions)
fit_protein_make_specs makes all specs ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 88 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (n-chains 88)
INFO:: Command: (chain_id 88 0)
INFO:: Command: (chain_id 88 1)
INFO:: Command: (setnum-from-serial-number 88 "A" 0)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 0)
INFO:: Command: (setnum-from-serial-number 88 "A" 1)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 1)
INFO:: Command: (setnum-from-serial-number 88 "A" 2)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 2)
INFO:: Command: (setnum-from-serial-number 88 "A" 3)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 3)
INFO:: Command: (setnum-from-serial-number 88 "A" 4)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 4)
INFO:: Command: (setnum-from-serial-number 88 "A" 5)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 5)
INFO:: Command: (setnum-from-serial-number 88 "A" 6)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 6)
INFO:: Command: (setnum-from-serial-number 88 "A" 7)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 7)
INFO:: Command: (setnum-from-serial-number 88 "A" 8)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 8)
INFO:: Command: (setnum-from-serial-number 88 "A" 9)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 9)
INFO:: Command: (setnum-from-serial-number 88 "A" 10)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 10)
INFO:: Command: (setnum-from-serial-number 88 "A" 11)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 11)
INFO:: Command: (setnum-from-serial-number 88 "A" 12)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 12)
INFO:: Command: (setnum-from-serial-number 88 "A" 13)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 13)
INFO:: Command: (setnum-from-serial-number 88 "A" 14)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 14)
INFO:: Command: (setnum-from-serial-number 88 "A" 15)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 15)
INFO:: Command: (setnum-from-serial-number 88 "A" 16)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 16)
INFO:: Command: (setnum-from-serial-number 88 "A" 17)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 17)
INFO:: Command: (setnum-from-serial-number 88 "A" 18)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 18)
INFO:: Command: (setnum-from-serial-number 88 "A" 19)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 19)
INFO:: Command: (setnum-from-serial-number 88 "A" 20)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 20)
INFO:: Command: (setnum-from-serial-number 88 "A" 21)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 21)
INFO:: Command: (setnum-from-serial-number 88 "A" 22)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 22)
INFO:: Command: (setnum-from-serial-number 88 "A" 23)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 23)
INFO:: Command: (setnum-from-serial-number 88 "A" 24)
INFO:: Command: (insertion-code-from-serial-number 88 "A" 24)
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INFO:: Command: (setnum-from-serial-number 88 "B" 95)
INFO:: Command: (insertion-code-from-serial-number 88 "B" 95)
   specs: 189 [[88, 'A', 1, ''], [88, 'A', 2, ''], [88, 'A', 3, ''], [88, 'A', 4, ''], [88, 'A', 5, ''], [88, 'A', 6, ''], [88, 'A', 7, ''], [88, 'A', 8, ''], [88, 'A', 9, ''], [88, 'A', 10, ''], [88, 'A', 11, ''], [88, 'A', 12, ''], [88, 'A', 13, ''], [88, 'A', 14, ''], [88, 'A', 15, ''], [88, 'A', 16, ''], [88, 'A', 17, ''], [88, 'A', 18, ''], [88, 'A', 19, ''], [88, 'A', 20, ''], [88, 'A', 21, ''], [88, 'A', 22, ''], [88, 'A', 23, ''], [88, 'A', 24, ''], [88, 'A', 25, ''], [88, 'A', 26, ''], [88, 'A', 27, ''], [88, 'A', 28, ''], [88, 'A', 29, ''], [88, 'A', 30, ''], [88, 'A', 31, ''], [88, 'A', 32, ''], [88, 'A', 33, ''], [88, 'A', 34, ''], [88, 'A', 35, ''], [88, 'A', 36, ''], [88, 'A', 37, ''], [88, 'A', 38, ''], [88, 'A', 39, ''], [88, 'A', 40, ''], [88, 'A', 41, ''], [88, 'A', 42, ''], [88, 'A', 43, ''], [88, 'A', 44, ''], [88, 'A', 45, ''], [88, 'A', 46, ''], [88, 'A', 47, ''], [88, 'A', 48, ''], [88, 'A', 49, ''], [88, 'A', 50, ''], [88, 'A', 51, ''], [88, 'A', 52, ''], [88, 'A', 53, ''], [88, 'A', 54, ''], [88, 'A', 55, ''], [88, 'A', 56, ''], [88, 'A', 57, ''], [88, 'A', 58, ''], [88, 'A', 59, ''], [88, 'A', 60, ''], [88, 'A', 61, ''], [88, 'A', 62, ''], [88, 'A', 63, ''], [88, 'A', 64, ''], [88, 'A', 65, ''], [88, 'A', 66, ''], [88, 'A', 67, ''], [88, 'A', 68, ''], [88, 'A', 69, ''], [88, 'A', 70, ''], [88, 'A', 71, ''], [88, 'A', 72, ''], [88, 'A', 73, ''], [88, 'A', 74, ''], [88, 'A', 75, ''], [88, 'A', 76, ''], [88, 'A', 77, ''], [88, 'A', 78, ''], [88, 'A', 79, ''], [88, 'A', 80, ''], [88, 'A', 81, ''], [88, 'A', 82, ''], [88, 'A', 83, ''], [88, 'A', 84, ''], [88, 'A', 85, ''], [88, 'A', 86, ''], [88, 'A', 87, ''], [88, 'A', 88, ''], [88, 'A', 89, ''], [88, 'A', 90, ''], [88, 'A', 91, ''], [88, 'A', 92, ''], [88, 'A', 93, ''], [88, 'B', 1, ''], [88, 'B', 2, ''], [88, 'B', 3, ''], [88, 'B', 4, ''], [88, 'B', 5, ''], [88, 'B', 6, ''], [88, 'B', 7, ''], [88, 'B', 8, ''], [88, 'B', 9, ''], [88, 'B', 10, ''], [88, 'B', 11, ''], [88, 'B', 12, ''], [88, 'B', 13, ''], [88, 'B', 14, ''], [88, 'B', 15, ''], [88, 'B', 16, ''], [88, 'B', 17, ''], [88, 'B', 18, ''], [88, 'B', 19, ''], [88, 'B', 20, ''], [88, 'B', 21, ''], [88, 'B', 22, ''], [88, 'B', 23, ''], [88, 'B', 24, ''], [88, 'B', 25, ''], [88, 'B', 26, ''], [88, 'B', 27, ''], [88, 'B', 28, ''], [88, 'B', 29, ''], [88, 'B', 30, ''], [88, 'B', 31, ''], [88, 'B', 32, ''], [88, 'B', 33, ''], [88, 'B', 34, ''], [88, 'B', 35, ''], [88, 'B', 36, ''], [88, 'B', 37, ''], [88, 'B', 38, ''], [88, 'B', 39, ''], [88, 'B', 40, ''], [88, 'B', 41, ''], [88, 'B', 42, ''], [88, 'B', 43, ''], [88, 'B', 44, ''], [88, 'B', 45, ''], [88, 'B', 46, ''], [88, 'B', 47, ''], [88, 'B', 48, ''], [88, 'B', 49, ''], [88, 'B', 50, ''], [88, 'B', 51, ''], [88, 'B', 52, ''], [88, 'B', 53, ''], [88, 'B', 54, ''], [88, 'B', 55, ''], [88, 'B', 56, ''], [88, 'B', 57, ''], [88, 'B', 58, ''], [88, 'B', 59, ''], [88, 'B', 60, ''], [88, 'B', 61, ''], [88, 'B', 62, ''], [88, 'B', 63, ''], [88, 'B', 64, ''], [88, 'B', 65, ''], [88, 'B', 66, ''], [88, 'B', 67, ''], [88, 'B', 68, ''], [88, 'B', 69, ''], [88, 'B', 70, ''], [88, 'B', 71, ''], [88, 'B', 72, ''], [88, 'B', 73, ''], [88, 'B', 74, ''], [88, 'B', 75, ''], [88, 'B', 76, ''], [88, 'B', 77, ''], [88, 'B', 78, ''], [88, 'B', 79, ''], [88, 'B', 80, ''], [88, 'B', 81, ''], [88, 'B', 82, ''], [88, 'B', 83, ''], [88, 'B', 84, ''], [88, 'B', 85, ''], [88, 'B', 86, ''], [88, 'B', 87, ''], [88, 'B', 88, ''], [88, 'B', 89, ''], [88, 'B', 90, ''], [88, 'B', 91, ''], [88, 'B', 92, ''], [88, 'B', 93, ''], [88, 'B', 94, ''], [88, 'B', 95, ''], [88, 'B', 96, '']]
ok
test54_0 (__main__.PdbMtzTestFunctions)
Phosphate distance in pucker analysis is sane ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2goz-manip.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2goz-manip.pdb
 PDB file /lmb/home/pemsley/data/greg-data/2goz-manip.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 7 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/85
Molecule 89 read successfully
DEBUG:: there were 7 types with no dictionary 
ok
test60_0 (__main__.PdbMtzTestFunctions)
post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok
test61_0 (__main__.PdbMtzTestFunctions)
Read/write gz coordinate files ... INFO:: Command: (write-pdb-file 0 "rnase_zip_test.pdb.gz")
INFO:: Command: (handle-read-draw-molecule-with-recentre "rnase_zip_test.pdb.gz" 1)

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe
INFO:: Reading coordinate file: rnase_zip_test.pdb.gz
 PDB file rnase_zip_test.pdb.gz has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 90 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: found bad VAL chiral atom: A 2   CB  
ok
test999_0 (__main__.PdbMtzTestFunctions)
Renumber residue range without overwriting coordinates. ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 91 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:35_2016_modification_0.pdb.gz
INFO:: Command: (renumber-residue-range 91 "A" 10 20 -55)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:35_2016_modification_1.pdb.gz
INFO:: Command: (renumber-residue-range 91 "A" 90 93 10)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:35_2016_modification_2.pdb.gz
INFO:: Command: (renumber-residue-range 91 "A" 89 91 1)
WARNING:: the new residue range overlaps with original one. Please change the range. Nothing has been done.
INFO:: Command: (renumber-residue-range 91 "A" 80 91 12)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:14:35_2016_modification_3.pdb.gz
INFO:: Command: (renumber-residue-range 91 "A" -100 200 9)
ok
test01_0 (__main__.ShelxTestFunctions)
Read small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/HOF.RES" 1)
SFAC LINE: SFAC C H N O S
INFO:: CELL set to 5.9028 13.6977 9.2374 90 98.211 90
READ-INS:: Spacegroup: "P 1 21/c 1"
INFO:: chain has 2 residues
Symmetry available for this molecule
Molecule 92 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/HOF.RES")
ok
test02_0 (__main__.ShelxTestFunctions)
Read hollander small molecule .res file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/hollander.ins" 1)
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O CO
INFO:: CELL set to 34.3243 34.3243 11.0887 90 90 90
READ-INS:: Spacegroup: "I 41 2 2"
INFO:: chain has 2 residues
Symmetry available for this molecule
Molecule 93 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/hollander.ins")
INFO:: spacegroup: I 41 2 2
ok
test03_0 (__main__.ShelxTestFunctions)
read shelx insulin with fcf ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/insulin.res" 1)
LATT LINE: LATT -2
SFAC LINE: SFAC  C  H  N  O  S
INFO:: CELL set to 77.726 77.726 77.726 90 90 90
READ-INS:: Spacegroup: "I 21 3"
INFO:: chain has 121 residues
Symmetry available for this molecule
Molecule 94 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/insulin.res")
Map statistics: mean: -5.07009e-05 st.d: 0.305174
Map statistics: min: -0.781031, max: 6.07907
  -0.69528    231
 -0.523777    4724
 -0.352275    24910
 -0.180772    55291
-0.00926962    95241
  0.162233    40930
  0.333735    7480
  0.505238    3968
   0.67674    2790
  0.848243    2117
   1.01975    1738
   1.19125    1221
   1.36275    888
   1.53425    595
   1.70576    355
   1.87726    240
   2.04876    137
   2.22026    97
   2.39177    62
   2.56327    46
   2.73477    17
   2.90627    17
   3.07778    13
   3.24928    10
   3.42078    7
   3.59228    1
   3.76379    3
   3.93529    7
   4.10679    2
   4.27829    5
    4.4498    1
    4.6213    2
    4.7928    2
    4.9643    0
   5.13581    1
   5.30731    0
   5.47881    0
   5.65031    0
   5.82182    0
   5.99332    1
   6.16482    0
Map statistics: mean: -1.00547e-05 st.d: 0.0468085
Map statistics: min: -0.211523, max: 0.648623
 -0.200772    7
 -0.179268    48
 -0.157764    209
 -0.136261    787
 -0.114757    2257
-0.0932533    5676
-0.0717496    12730
 -0.050246    24380
-0.0287423    38191
-0.00723865    46229
  0.014265    43880
 0.0357687    32484
 0.0572723    19420
  0.078776    9718
   0.10028    4120
  0.121783    1677
  0.143287    718
  0.164791    329
  0.186294    133
  0.207798    77
  0.229302    29
  0.250805    11
  0.272309    13
  0.293813    8
  0.315316    2
   0.33682    2
  0.358324    2
  0.379827    1
  0.401331    1
  0.422835    2
  0.444338    2
  0.465842    1
  0.487346    1
  0.508849    1
  0.530353    1
  0.551857    1
   0.57336    0
  0.594864    0
  0.616368    0
  0.637871    2
  0.659375    0
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
ok
test04_0 (__main__.ShelxTestFunctions)
Write an INS from PDB test ... 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.
ok
test05_0 (__main__.ShelxTestFunctions)
new molecule by atom selection inherits shelx molecule flag ... Symmetry available for this molecule
INFO:: Command: (update-go-to-atom-window-on-new-mol)
ok
test06_0 (__main__.ShelxTestFunctions)
Addition of Terminal Residue on SHELX molecule has correct occupancy ... Symmetry available for this molecule
INFO:: Command: (update-go-to-atom-window-on-new-mol)
INFO:: Masking around 32 atoms
fitting terminal residue with 1000 random trials
--- in best_fit_phi_psi() with offset 1
INFO:: Fitting terminal residue  without individual rigid body fitting.
--- in best_fit_phi_psi() calling fit_terminal_residue_generic() with n_trials 1000
                     called fit_terminal_residue_generic() residue-seqnum: 2020 offset: 1
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/atom_selection_from_insulin.res_Tue_Dec_27_04:14:37_2016_modification_0.res
ERROR transfering AFIX back
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " N  "
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CA "
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " C  "
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " O  "
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CB "
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CG "
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " ND1"
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CE1"
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " NE2"
WARNING:: failed to get AFIX handle for "" 2010 "HIS" " CD2"
INFO:: Command: (add-terminal-residue 98 "B" 2020 1)
ok
test07_0 (__main__.ShelxTestFunctions)
Add water to SHELX molecule ... INFO:: Command: (set-rotation-centre  3.00 -1.00 60.00)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Tue_Dec_27_04:14:37_2016_modification_0.res
1/D/3069 {HOH}/ O   altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule
INFO:: Command: (place-typed-atom-at-pointer "Water")
INFO:: Command: (resname-from-serial-number 94 "D" 68)
INFO:: Command: (setnum-from-serial-number 94 "D" 68)
INFO:: Command: (insertion-code-from-serial-number 94 "D" 68)
ok
test08_0 (__main__.ShelxTestFunctions)
Find Waters for a SHELXL molecule ... INFO:: Command: (n-chains 94)
INFO:: Protein centre at: xyz = (   -0.2998,      10.6,     57.56)
using sigma cut off 0.6
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.305174
INFO:: Using density cut-off: 0.183104 (0.6 sigma)  (mean -0.0203497 stdev: 0.111926)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
-------------------------------------------------------------
INFO:: cluster at xyz = (    -4.859,      20.8,      69.7) is too big to be water
INFO:: cluster at xyz = (     4.249,    -1.354,     48.69) is too big to be water
INFO:: cluster at xyz = (   0.05491,      16.3,     69.67) is too big to be water
INFO:: cluster at xyz = (     15.59,      8.13,     53.24) is too big to be water
INFO:: cluster at xyz = (     20.55,     4.875,     65.84) is too big to be water
INFO:: cluster at xyz = (    -5.054,     9.822,     69.12) is too big to be water
INFO:: found 28 waters in water fitting
Done - back from lig.water_fit()
DEBUG::  new_waters_mol_flag: 0
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_insulin.res_Tue_Dec_27_04:14:37_2016_modification_1.res
ERROR transfering AFIX back
WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O  "
INFO:: Adding to solvent chain: D
INFO:: Command: (n-chains 94)
INFO:: Command: (resname-from-serial-number 94 "D" 96)
INFO:: Command: (setnum-from-serial-number 94 "D" 96)
INFO:: Command: (insertion-code-from-serial-number 94 "D" 96)
ok
test09_0 (__main__.ShelxTestFunctions)
NPD Anisotropic Atom [Mitch Miller] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/miller/shelx-test4-NPD-mini.res" 1)
LATT LINE: LATT -1
SFAC LINE: SFAC  C  H  N  O  S  SE  CL
WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3:
INFO:: CELL set to 42.14 83.03 89.79 90 90 90
READ-INS:: Spacegroup: "P 21 21 21"
INFO:: chain has 5 residues
Symmetry available for this molecule
Molecule 99 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/miller/shelx-test4-NPD-mini.res")
INFO:: Command: (close-molecule 99)
ok
test10_0 (__main__.ShelxTestFunctions)
close shelx molecules ... INFO:: Command: (close-molecule 95)
INFO:: Command: (close-molecule 94)
ok
test11_0 (__main__.ShelxTestFunctions)
Aniso Bs in P21 ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/horma-p21.res" 1)
LATT LINE: LATT -1
SFAC LINE: SFAC C H N O MG CL
INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90
READ-INS:: Spacegroup: "P 1 21 1"
INFO:: chain has 23 residues
Symmetry available for this molecule
Molecule 100 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/horma-p21.res")
INFO:: SHELXL file new-horma.ins written.
INFO:: Command: (handle-read-draw-molecule-with-recentre "new-horma.ins" 1)
LATT LINE: LATT -1
SFAC LINE: SFAC  C  H  N  O  MG  CL
INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90
READ-INS:: Spacegroup: "P 1 21 1"
INFO:: chain has 23 residues
Symmetry available for this molecule
Molecule 101 read successfully
INFO:: Command: (read-shelx-ins-file "new-horma.ins")
b_1: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066]
b_2: [3.5066084720723203, 0.02956785245047131, 0.06022999999999999, 0.04343729760622815, 0.0005615499559004258, -0.006816141456079681, -0.0034269077402606066]
ok
test12_0 (__main__.ShelxTestFunctions)
Don't crash on reading a strange HAT file ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/crash.hat" 0)
LATT LINE: LATT -2
SFAC LINE: SFAC S
INFO:: CELL set to 108.999 108.999 107.555 90 90 90
READ-INS:: Spacegroup: "I 4 2 2"
INFO:: chain has 4 residues
Symmetry available for this molecule
Molecule 102 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/crash.hat")
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/crash.hat" 1)
LATT LINE: LATT -2
SFAC LINE: SFAC S
INFO:: CELL set to 108.999 108.999 107.555 90 90 90
READ-INS:: Spacegroup: "I 4 2 2"
INFO:: chain has 4 residues
Symmetry available for this molecule
Molecule 103 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/crash.hat")
ok
test01_0 (__main__.LigandTestFunctions)
Get monomer test ... INFO:: Command: (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 0)
INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 104 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:14:37_2016_modification_0.pdb.gz
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:14:37_2016_modification_1.pdb.gz
INFO:: Command: (delete-residue-hydrogens 104 "A" 1 "" "")
ok
test02_0 (__main__.LigandTestFunctions)
Set Bond thickness test ... ok
test03_0 (__main__.LigandTestFunctions)
Delete all-molecule Hydrogens ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 105 read successfully
DEBUG:: there were 0 types with no dictionary 
here 1
ok
test04_0 (__main__.LigandTestFunctions)
Non-Autoloads ... INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
WARNING:: can't find LIG in monomer dictionary
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-LIG.pdb
 PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 106 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 
WARNING:: can't find LIG in monomer dictionary
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/test-LIG.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/test-LIG.pdb
 PDB file /lmb/home/pemsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 107 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
WARNING:: can't find LIG in monomer dictionary
ok
test05_0 (__main__.LigandTestFunctions)
Move and Refine Ligand test ... INFO:: Command: (go-to-view-number 2 1)
INFO:: Command: (set-rotation-centre 55.30  9.10 20.60)
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:14:37_2016_modification_2.pdb.gz
INFO:: Command: (backup-state 104)
INFO:: Command: (turn-off-backup 104)
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: Command: (turn-on-backup 104)
ok
test06_0 (__main__.LigandTestFunctions)
Many Molecules - Ligand Fitting ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb" 0)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 108 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
INFO:: Command: (copy-molecule 108)
Symmetry available for this molecule
INFO:: Command: (copy-molecule 108)
Symmetry available for this molecule
INFO:: Command: (copy-molecule 108)
Symmetry available for this molecule
INFO:: Command: (copy-molecule 108)
Symmetry available for this molecule
INFO:: Command: (copy-molecule 108)
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
 PDB file /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 0/113
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 0/117
  INFO:: fill_ghost_info Constructed 6 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain A"
      Ghost 1 name: "NCS found from matching Chain E onto Chain A"
      Ghost 2 name: "NCS found from matching Chain G onto Chain A"
      Ghost 3 name: "NCS found from matching Chain D onto Chain B"
      Ghost 4 name: "NCS found from matching Chain F onto Chain B"
      Ghost 5 name: "NCS found from matching Chain H onto Chain B"
Molecule 114 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: making conventional map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.243 seconds to read MTZ file
INFO:: 0.149 seconds to initialize map
INFO:: 0.116 seconds for FFT
INFO:: 0.022 seconds for statistics
      Map mean: ........ -8.79008e-07
      Map sigma: ....... 0.171188
      Map maximum: ..... 1.34304
      Map minimum: ..... -0.695441
INFO:: 0.01 seconds for contour map
INFO:: 0.54 seconds in total
INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0  0.00  0.00)
INFO:: making difference map from MTZ filename /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT
Number of OBSERVED reflections: 54440
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 160, 160, 336)
INFO:: 0.145 seconds to read MTZ file
INFO:: 0.002 seconds to initialize map
INFO:: 0.113 seconds for FFT
INFO:: 0.022 seconds for statistics
      Map mean: ........ 2.09389e-06
      Map sigma: ....... 0.0333923
      Map maximum: ..... 0.366077
      Map minimum: ..... -0.191665
INFO:: 0.005 seconds for contour map
INFO:: 0.287 seconds in total
INFO:: Command: (make-and-draw-map-with-reso-with-refmac-params "/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "DELFWT" "PHDELWT" "" 0 1 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0  0.00  0.00)
INFO:: ligand number 0 is molecule number 108   with wiggly flag: 0
ligand_search_install_wiggly_ligands: returning wlig 0x2a58c300
Executing ligand search internal using wlig_p 0x2a58c300
in execute_ligand_search_internal() import maps from mol 115
INFO:: Protein centre at: xyz = (     58.29,     34.65,     30.63)
Map statistics: mean: -0.0216745 st.d: 0.0886263
Map statistics: min: -0.695441, max: 0.754209
  -0.67732    6
 -0.641079    8
 -0.604838    27
 -0.568596    116
 -0.532355    354
 -0.496114    977
 -0.459873    1943
 -0.423631    3356
  -0.38739    5156
 -0.351149    6576
 -0.314908    7850
 -0.278666    8875
 -0.242425    9742
 -0.206184    11742
 -0.169943    16950
 -0.133701    29805
-0.0974601    58214
-0.0612188    102890
-0.0249776    142998
 0.0112637    471775
 0.0475049    106846
 0.0837462    56087
  0.119987    21597
  0.156229    6911
   0.19247    2135
  0.228711    920
  0.264952    467
  0.301194    346
  0.337435    216
  0.373676    118
  0.409917    117
  0.446159    80
    0.4824    50
  0.518641    28
  0.554882    33
  0.591124    15
  0.627365    14
  0.663606    11
  0.699847    2
  0.736089    7
   0.77233    0
INFO:: find_clusters map_rms is 0.171132
INFO:: Using density cut-off: 0.171132 (1 sigma)  (mean -0.0216776 stdev: 0.0886191)
INFO:: Blobs with volume larger than 11 A^3 are too big to be considered waters.
INFO:: Using water to protein distance limits: 2.4 3.2
INFO:: Finding clusters...done
debug:: n_ligands_for_cluster() top_score 4.04177 and 4 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.0066 and 9 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.09237 and 4 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.85663 and 6 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.38681 and 10 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.61147 and 8 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.10047 and 8 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.69083 and 7 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 2.12333 and 2 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
debug:: n_ligands_for_cluster() top_score 1.84146 and 6 are decent out of 12
Symmetry available for this molecule
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
   Fitting NPO gave these results:  [118, 119, 120, 121, 122, 123, 124, 125, 126, 127]
ok
test07_0 (__main__.LigandTestFunctions)
Flip residue (around eigen vectors) ... INFO:: Command: (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 1)
INFO:: Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 128 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
INFO:: Command: (copy-molecule 128)
INFO:: Command: (set-go-to-atom-molecule 128)
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:14:57_2016_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
distance:  4.05825912267
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:14:57_2016_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:14:57_2016_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Tue_Dec_27_04:14:57_2016_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
distance d2:  1.60332907424e-07
ok
test08_0 (__main__.LigandTestFunctions)
Test dipole ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/dipole-residues.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/dipole-residues.pdb
 PDB file /lmb/home/pemsley/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 130 read successfully
DEBUG:: there were 0 types with no dictionary 
info:: dipole components [-2.219999939203263, 4.440892098500626e-16, 0.0]
ok
test09_0 (__main__.LigandTestFunctions)
Reading new dictionary restraints replaces ... WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib, file "/lmb/home/pemsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif had no bond restraints
ok
test10_0 (__main__.LigandTestFunctions)
Pyrogen Runs OK? ... ok
test01_0 (__main__.CootaneerTestFunctions)
Assignment of new PIR sequence overwrites old assignment ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 131 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 131
INFO:: Command: (assign-pir-sequence 131 "A" ">test

ACDEFGHIKLMNPQ*")
debug seq ACDEFGHIKLMNPQ
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 131
INFO:: Command: (assign-pir-sequence 131 "A" ">test

ACDEFGHIKLMNPQRST*")
ok
test02_0 (__main__.CootaneerTestFunctions)
Cootaneer Beta Strand ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb
 PDB file /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 132 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.047 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.026 seconds for FFT
INFO:: 0.005 seconds for statistics
      Map mean: ........ 1.06932e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.022 seconds for contour map
INFO:: 0.101 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 132
INFO:: Command: (assign-pir-sequence 132 "A" "> tutorial-modern chain A
RNASE
DVSGTVCLSA LPPEATDTLN LIASDGPFPY SQDGVVFQNR ESVLPTQSYG 
YYHEYTVITP GARTRGTRRI ICGEATQEDY YTGDHYATFS LID * 

")
INFO:: Command: (set-rotation-centre 64.27  7.04 14.42)
   Cootaneering: imol 132 chain-id B resno 60 inscode  at-name  CA  alt-conf 

Sequence: ?EYTVITPGARTR
Confidence: 0.999999

From    : HEYTVITPGARTR
Chain id: 0	Offset: 53
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Tue_Dec_27_04:15:01_2016_modification_0.pdb.gz
bypassing ? at 0
Mutating to GLU at 1
Mutating poly_ala residue number 58
Mutating to TYR at 2
Mutating poly_ala residue number 59
Mutating to THR at 3
Mutating poly_ala residue number 60
Mutating to VAL at 4
Mutating poly_ala residue number 61
Mutating to ILE at 5
Mutating poly_ala residue number 62
Mutating to THR at 6
Mutating poly_ala residue number 63
Mutating to PRO at 7
Mutating poly_ala residue number 64
Mutating to GLY at 8
Mutating poly_ala residue number 65
Mutating to ALA at 9
Mutating poly_ala residue number 66
Mutating to ARG at 10
Mutating poly_ala residue number 67
Mutating to THR at 11
Mutating poly_ala residue number 68
Mutating to ARG at 12
Mutating poly_ala residue number 69
DEBUG:: Creating a new chain B
WARNING:: no rotamers probabilities for residue type GLY
INFO:: replace_coords: 9 atoms updated.
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
INFO:: replace_coords: 12 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 8 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 7 atoms updated.
WARNING:: no rotamers probabilities for residue type GLY
WARNING:: no rotamers probabilities for residue type ALA
INFO:: replace_coords: 11 atoms updated.
INFO:: replace_coords: 7 atoms updated.
INFO:: replace_coords: 11 atoms updated.
ok
test01_0 (__main__.RnaGhostsTestFunctions)
RNA NCS Ghosts ... INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.0120681
    rms devi: 0.0134464
    max devi: 0.0214179
    min devi: 0.00385596
INFO:: 5 matched atoms had: 
   mean devi: 0.270216
    rms devi: 0.335002
    max devi: 0.536002
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.26738
    rms devi: 0.322791
    max devi: 0.495136
    min devi: 0.112289
INFO:: 5 matched atoms had: 
   mean devi: 0.270247
    rms devi: 0.335033
    max devi: 0.536044
    min devi: 0.0847029
INFO:: 5 matched atoms had: 
   mean devi: 0.267411
    rms devi: 0.322823
    max devi: 0.495177
    min devi: 0.112221
INFO:: 5 matched atoms had: 
   mean devi: 0.011982
    rms devi: 0.013349
    max devi: 0.0212578
    min devi: 0.0038732
INFO:: 5 matched atoms had: 
   mean devi: 0.000242576
    rms devi: 0.000242751
    max devi: 0.000256671
    min devi: 0.000231275
INFO:: 5 matched atoms had: 
   mean devi: 0.270185
    rms devi: 0.334971
    max devi: 0.535961
    min devi: 0.0845571
INFO:: 5 matched atoms had: 
   mean devi: 0.267349
    rms devi: 0.322759
    max devi: 0.495094
    min devi: 0.112357
INFO:: 5 matched atoms had: 
   mean devi: 6.9313e-05
    rms devi: 6.93629e-05
    max devi: 7.33402e-05
    min devi: 6.60841e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.0120334
    rms devi: 0.0134072
    max devi: 0.0213538
    min devi: 0.00386188
INFO:: 5 matched atoms had: 
   mean devi: 0.000138622
    rms devi: 0.000138721
    max devi: 0.000146676
    min devi: 0.000132164
INFO:: 5 matched atoms had: 
   mean devi: 0.011999
    rms devi: 0.0133684
    max devi: 0.0212898
    min devi: 0.0038691
INFO:: 5 matched atoms had: 
   mean devi: 0.267426
    rms devi: 0.322839
    max devi: 0.495197
    min devi: 0.112187
INFO:: 5 matched atoms had: 
   mean devi: 0.270294
    rms devi: 0.335079
    max devi: 0.536106
    min devi: 0.0848122
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Tue_Dec_27_04:15:02_2016_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: Command: (copy-molecule 134)
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
INFO:: Command: (set-rotation-centre 76.27 10.04 14.42)
INFO:: Command: (go-to-view-number 3 1)
INFO:: Command: (n-chains 135)
INFO:: Command: (chain_id 135 0)
INFO:: Command: (chain_id 135 1)
INFO:: Command: (is-solvent-chain-p 135 "A")
   There are 8 residues in chain A
INFO:: Command: (resname-from-serial-number 135 "A" 0)
INFO:: Command: (setnum-from-serial-number 135 "A" 0)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 0)
INFO:: Command: (resname-from-serial-number 135 "A" 1)
INFO:: Command: (setnum-from-serial-number 135 "A" 1)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 1)
INFO:: Command: (resname-from-serial-number 135 "A" 2)
INFO:: Command: (setnum-from-serial-number 135 "A" 2)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 2)
INFO:: Command: (resname-from-serial-number 135 "A" 3)
INFO:: Command: (setnum-from-serial-number 135 "A" 3)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 3)
INFO:: Command: (resname-from-serial-number 135 "A" 4)
INFO:: Command: (setnum-from-serial-number 135 "A" 4)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 4)
INFO:: Command: (resname-from-serial-number 135 "A" 5)
INFO:: Command: (setnum-from-serial-number 135 "A" 5)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 5)
INFO:: Command: (resname-from-serial-number 135 "A" 6)
INFO:: Command: (setnum-from-serial-number 135 "A" 6)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 6)
INFO:: Command: (resname-from-serial-number 135 "A" 7)
INFO:: Command: (setnum-from-serial-number 135 "A" 7)
INFO:: Command: (insertion-code-from-serial-number 135 "A" 7)
INFO:: Command: (is-solvent-chain-p 135 "B")
   There are 8 residues in chain B
INFO:: Command: (resname-from-serial-number 135 "B" 0)
INFO:: Command: (setnum-from-serial-number 135 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 0)
INFO:: Command: (resname-from-serial-number 135 "B" 1)
INFO:: Command: (setnum-from-serial-number 135 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 1)
INFO:: Command: (resname-from-serial-number 135 "B" 2)
INFO:: Command: (setnum-from-serial-number 135 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 2)
INFO:: Command: (resname-from-serial-number 135 "B" 3)
INFO:: Command: (setnum-from-serial-number 135 "B" 3)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 3)
INFO:: Command: (resname-from-serial-number 135 "B" 4)
INFO:: Command: (setnum-from-serial-number 135 "B" 4)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 4)
INFO:: Command: (resname-from-serial-number 135 "B" 5)
INFO:: Command: (setnum-from-serial-number 135 "B" 5)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 5)
INFO:: Command: (resname-from-serial-number 135 "B" 6)
INFO:: Command: (setnum-from-serial-number 135 "B" 6)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 6)
INFO:: Command: (resname-from-serial-number 135 "B" 7)
INFO:: Command: (setnum-from-serial-number 135 "B" 7)
INFO:: Command: (insertion-code-from-serial-number 135 "B" 7)
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: Command: (copy-molecule 134)
INFO:: Matching/moving molecule number 136 to 136
INFO:: LSQ matched 125 atoms
INFO:: 125 matched atoms had: 
   mean devi: 2.34078e-06
    rms devi: 2.50408e-06
    max devi: 4.30573e-06
    min devi: 6.25954e-07
INFO:: Axis orientation: (   -0.2159,   -0.1334,    0.9673)
INFO:: Rotation in CCP4 Polar Angles: Polar = (     0,     0,     0)
INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Tue_Dec_27_04:15:03_2016_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|         1, 1.299e-08, 1.791e-09|
|-1.299e-08,         1,-2.899e-09|
|-1.791e-09, 2.899e-09,         1|
(    -24.06,    -24.06,    -24.06)
No unit cell for this molecule, hence no fractional matrix.
INFO:: Command: (go-to-view-number 4 1)
ok
test01_0 (__main__.SsmTestFunctions)
SSM - Frank von Delft's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/1wly.pdb" 0)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1wly.pdb
 PDB file /lmb/home/pemsley/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 137 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/1yb5.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/1yb5.pdb
 PDB file /lmb/home/pemsley/data/greg-data/1yb5.pdb has been read.
Spacegroup: P 21 21 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 324/324
INFO:: NCS chain comparison 0/324
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 138 read successfully
DEBUG:: there were 2 types with no dictionary 
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion()
INFO:: Command: (graphics-to-ca-plus-ligands-representation 137)
INFO:: Command: (graphics-to-ca-plus-ligands-representation 138)
INFO:: reference 137 has 750 atoms selected
INFO:: moving    138 has 842 atoms selected
superposing...
number of Ca atoms in selections: 110 (moving) and 100 (reference)
Another Go...

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

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

 Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY
 Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI

INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_1yb5.pdb_Tue_Dec_27_04:15:04_2016_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 
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%
INFO:: Command: (set-rotation-centre 65.65 -3.00 -4.00)
INFO:: Command: (go-to-view-number 5 1)
ok
test02_0 (__main__.SsmTestFunctions)
SSM - Alice Dawson's Example ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/1pyd.pdb" 0)
WARNING:: Error reading /lmb/home/pemsley/data/greg-data/1pyd.pdb
INFO:: Command: (graphics-to-ca-plus-ligands-representation -1)
INFO:: Command: (set-graphics-window-size 678 452)
INFO:: Command: (molecule-name 0)
    0    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 1)
    1    /lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb
    2    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
    3    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 4)
    4    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 5)
    5    mainchain
INFO:: Command: (molecule-name 6)
    6    /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb
INFO:: Command: (molecule-name 7)
    7    regression-test-terminal-residue.pdb
INFO:: Command: (molecule-name 8)
    8    atom selection from regression-test-terminal-residue.pdb
INFO:: Command: (molecule-name 9)
    9    /lmb/home/pemsley/data/greg-data/frag-2wot.pdb
INFO:: Command: (molecule-name 10)
    10    sphere selection from tutorial-modern.pdb
INFO:: Command: (molecule-name 11)
    11    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 13)
    13    /lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb
INFO:: Command: (molecule-name 14)
    14    /lmb/home/pemsley/data/greg-data/res098.pdb
INFO:: Command: (molecule-name 15)
    15    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
    16    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 17)
    17    /lmb/home/pemsley/data/greg-data/pdb3knw.ent
INFO:: Command: (molecule-name 18)
    18    /lmb/home/pemsley/data/greg-data/pdb1py3.ent
INFO:: Command: (molecule-name 21)
    21    /lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb
INFO:: Command: (molecule-name 22)
    22    /lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb
INFO:: Command: (molecule-name 23)
    23    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
    24    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 25)
    25    /lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb
INFO:: Command: (molecule-name 26)
    26    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
    27    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 28)
    28    /lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb
INFO:: Command: (molecule-name 29)
    29    /lmb/home/pemsley/data/greg-data/backrub-fragment.pdb
INFO:: Command: (molecule-name 30)
    30    Copy_of_/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb
    31    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT
INFO:: Command: (molecule-name 32)
    32    /lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb
INFO:: Command: (molecule-name 33)
    33    /lmb/home/pemsley/data/greg-data/val.pdb
INFO:: Command: (molecule-name 34)
    34    /lmb/home/pemsley/data/greg-data/2yie-frag.pdb
INFO:: Command: (molecule-name 35)
    35    /lmb/home/pemsley/data/greg-data/4f8g.pdb
INFO:: Command: (molecule-name 36)
    36    /lmb/home/pemsley/data/greg-data/4f8g.pdb
    37    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
    38    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 39)
    39    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
    40    Generic Masked Map
    41    difference-map
    44    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
    45    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
    46    averaged-map
    47    difference-map
INFO:: Command: (molecule-name 48)
    48    /lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb
INFO:: Command: (molecule-name 49)
    49    /lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb
    50    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 51)
    51    /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb
INFO:: Command: (molecule-name 52)
    52    /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb
INFO:: Command: (molecule-name 53)
    53    atom selection from tutorial-modern.pdb
INFO:: Command: (molecule-name 54)
    54    /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
INFO:: Command: (molecule-name 55)
    55    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 56)
    56    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 57)
    57    atom selection from tutorial-modern.pdb
INFO:: Command: (molecule-name 58)
    58    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 59)
    59    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 60)
    60    /lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb
INFO:: Command: (molecule-name 61)
    61    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 62)
    62    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 63)
    63    /lmb/home/pemsley/data/greg-data/pdb3hfl.ent
    64    /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT
INFO:: Command: (molecule-name 65)
    65    Ideal-A-form-RNA
INFO:: Command: (molecule-name 66)
    66    Ideal-A-form-RNA
INFO:: Command: (molecule-name 67)
    67    Ideal-A-form-DNA
INFO:: Command: (molecule-name 68)
    68    Ideal-A-form-DNA
INFO:: Command: (molecule-name 69)
    69    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 70)
    70    /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb
INFO:: Command: (molecule-name 71)
    71    /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb
INFO:: Command: (molecule-name 72)
    72    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 73)
    73    /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb
INFO:: Command: (molecule-name 74)
    74    /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb
INFO:: Command: (molecule-name 75)
    75    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
    76    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 77)
    77    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 78)
    78    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 79)
    79    /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
INFO:: Command: (molecule-name 80)
    80    /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
INFO:: Command: (molecule-name 81)
    81    /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 82)
    82    SymOp_-X,-X+Y,-Z+1/3_Copy_of_79
INFO:: Command: (molecule-name 83)
    83    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 84)
    84    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 85)
    85    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 86)
    86    /lmb/home/pemsley/data/greg-data/pdb1py3.ent
INFO:: Command: (molecule-name 87)
    87    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 88)
    88    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 89)
    89    /lmb/home/pemsley/data/greg-data/2goz-manip.pdb
INFO:: Command: (molecule-name 90)
    90    rnase_zip_test.pdb.gz
INFO:: Command: (molecule-name 91)
    91    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 92)
    92    /lmb/home/pemsley/data/greg-data/HOF.RES
INFO:: Command: (molecule-name 93)
    93    /lmb/home/pemsley/data/greg-data/hollander.ins
    96    /lmb/home/pemsley/data/greg-data/insulin.fcf Diff-SigmaA
INFO:: Command: (molecule-name 97)
    97    atom selection from insulin.res
INFO:: Command: (molecule-name 98)
    98    atom selection from insulin.res
INFO:: Command: (molecule-name 100)
    100    /lmb/home/pemsley/data/greg-data/horma-p21.res
INFO:: Command: (molecule-name 101)
    101    new-horma.ins
INFO:: Command: (molecule-name 102)
    102    /lmb/home/pemsley/data/greg-data/crash.hat
INFO:: Command: (molecule-name 103)
    103    /lmb/home/pemsley/data/greg-data/crash.hat
INFO:: Command: (molecule-name 104)
    104    coot-ccp4/monomer-3GP.pdb
INFO:: Command: (molecule-name 105)
    105    /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb
INFO:: Command: (molecule-name 106)
    106    /lmb/home/pemsley/data/greg-data/test-LIG.pdb
INFO:: Command: (molecule-name 107)
    107    /lmb/home/pemsley/data/greg-data/test-LIG.pdb
INFO:: Command: (molecule-name 108)
    108    /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 109)
    109    Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 110)
    110    Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 111)
    111    Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 112)
    112    Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 113)
    113    Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 114)
    114    /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
    115    /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT
    116    /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT
    117    Masked (by protein)
INFO:: Command: (molecule-name 118)
    118    Fitted ligand #0-0
INFO:: Command: (molecule-name 119)
    119    Fitted ligand #1-0
INFO:: Command: (molecule-name 120)
    120    Fitted ligand #2-0
INFO:: Command: (molecule-name 121)
    121    Fitted ligand #3-0
INFO:: Command: (molecule-name 122)
    122    Fitted ligand #4-0
INFO:: Command: (molecule-name 123)
    123    Fitted ligand #5-0
INFO:: Command: (molecule-name 124)
    124    Fitted ligand #6-0
INFO:: Command: (molecule-name 125)
    125    Fitted ligand #7-0
INFO:: Command: (molecule-name 126)
    126    Fitted ligand #8-0
INFO:: Command: (molecule-name 127)
    127    Fitted ligand #9-0
INFO:: Command: (molecule-name 128)
    128    coot-ccp4/monomer-3GP.pdb
INFO:: Command: (molecule-name 129)
    129    Copy_of_coot-ccp4/monomer-3GP.pdb
INFO:: Command: (molecule-name 130)
    130    /lmb/home/pemsley/data/greg-data/dipole-residues.pdb
INFO:: Command: (molecule-name 131)
    131    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 132)
    132    /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb
    133    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 134)
    134    Ideal-A-form-RNA
INFO:: Command: (molecule-name 135)
    135    Copy_of_Ideal-A-form-RNA
INFO:: Command: (molecule-name 136)
    136    Copy_of_Ideal-A-form-RNA
INFO:: Command: (molecule-name 137)
    137    /lmb/home/pemsley/data/greg-data/1wly.pdb
INFO:: Command: (molecule-name 138)
    138    /lmb/home/pemsley/data/greg-data/1yb5.pdb
INFO:: Command: (graphics-to-ca-plus-ligands-representation 138)
ok
test03_0 (__main__.SsmTestFunctions)
SSM by atom selection [JED Example] ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2qd9.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2qd9.pdb
 PDB file /lmb/home/pemsley/data/greg-data/2qd9.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 139 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/2gtn.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/2gtn.pdb
 PDB file /lmb/home/pemsley/data/greg-data/2gtn.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 0/337
Molecule 140 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: reference 139 has 169 atoms selected
INFO:: moving    140 has 169 atoms selected
superposing...
number of Ca atoms in selections: 21 (moving) and 21 (reference)
Another Go...

     Moving      Reference   Distance(/A)
      A 140  <--->  A 140  :  0.1804
      A 141  <--->  A 141  :  0.0760
      A 142  <--->  A 142  :  0.1052
      A 143  <--->  A 143  :  0.1246
      A 144  <--->  A 144  :  0.1370
      A 145  <--->  A 145  :  0.1380
      A 146  <--->  A 146  :  0.1662
      A 147  <--->  A 147  :  0.2744
      A 148  <--->  A 148  :  0.2728
      A 149  <--->  A 149  :  0.1173
      A 150  <--->  A 150  :  0.1684
      A 151  <--->  A 151  :  0.0928
      A 152  <--->  A 152  :  0.1200
      A 153  <--->  A 153  :  0.1281
      A 154  <--->  A 154  :  0.2539
      A 155  <--->  A 155  :  0.6351
      A 156  <--->  A 156  :  0.1300
      A 157  <--->  A 157  :  0.1478
      A 158  <--->  A 158  :  0.2238
      A 159  <--->  A 159  :  0.2271
      A 160  <--->  A 160  :  0.2372

 Moving: YIHSADIIHRDLKPSNLAVNE
 Target: YIHSADIIHRDLKPSNLAVNE

INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_2gtn.pdb_Tue_Dec_27_04:15:06_2016_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%
ok
test01_1 (__main__.NcsTestFunctions)
NCS maps test ... INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz
Number of OBSERVED reflections: 17939
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 108, 132,  64)
INFO:: 0.0450 seconds to read MTZ file
INFO:: 0.0010 seconds to initialize map
INFO:: 0.0260 seconds for FFT
INFO:: 0.0040 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 2.9776
      Map minimum: ..... -0.8750
INFO:: 0.0230 seconds for contour map
INFO:: 0.0990 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 2 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:: 409600 out of 409600 (100.0000%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: 0.0006 st.d: 0.3256
Map statistics: min: -1.4696, max: 2.2923
   -1.4225    2
   -1.3285    5
   -1.2344    5
   -1.1404    10
   -1.0463    9
   -0.9523    37
   -0.8583    141
   -0.7642    493
   -0.6702    1554
   -0.5761    4667
   -0.4821    12350
   -0.3880    26465
   -0.2940    43650
   -0.1999    55555
   -0.1059    57553
   -0.0118    50690
    0.0822    40145
    0.1763    30074
    0.2703    23268
    0.3644    17859
    0.4584    13062
    0.5524    9524
    0.6465    7028
    0.7405    4917
    0.8346    3611
    0.9286    2439
    1.0227    1610
    1.1167    1087
    1.2108    736
    1.3048    442
    1.3989    252
    1.4929    160
    1.5870    83
    1.6810    49
    1.7751    24
    1.8691    17
    1.9631    13
    2.0572    4
    2.1512    5
    2.2453    4
    2.3393    1
INFO:: installing ghost map with name :Map 141 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
ok
test02_0 (__main__.NcsTestFunctions)
NCS chains info ...    NCS info:  [['A', 'B']]
ok
test03_0 (__main__.NcsTestFunctions)
NCS deviation info ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/insulin.res" 1)
LATT LINE: LATT -2
SFAC LINE: SFAC  C  H  N  O  S
INFO:: CELL set to 77.7260 77.7260 77.7260 90.0000 90.0000 90.0000
READ-INS:: Spacegroup: "I 21 3"
INFO:: chain has 121 residues
Symmetry available for this molecule
Molecule 146 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/insulin.res")
no diffs
NCS target chain has 93 peers.
ok
test04_0 (__main__.NcsTestFunctions)
NCS Residue Range copy ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 147 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:15:09_2016_modification_0.pdb.gz
INFO:: Command: (delete-residue 147 "B" 1 "")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:15:09_2016_modification_1.pdb.gz
INFO:: Command: (delete-residue 147 "B" 2 "")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:15:09_2016_modification_2.pdb.gz
INFO:: Command: (delete-residue 147 "B" 3 "")
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: 147 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 147 and ichain: 0
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 0
   Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 90/93
First atom of 720 in first  selection 1/A/1 {ASP}/ N   altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 724 in second selection 1/B/4 {GLY}/ N   altLoc :: segid :: pos: (18.1830,22.2640,18.9300) B-factor: 21.7100
INFO:: LSQ matched 90 atoms
INFO:: 90 matched atoms had: 
   mean devi: 0.3643
    rms devi: 0.4571
    max devi: 2.1351
    min devi: 0.0881
   find_ncs_matrix returns (LSQ) 
|    0.9705,  -0.04634,   -0.2366|
|    0.2357,    0.3884,    0.8908|
|   0.05061,   -0.9203,    0.3878|
(      37.8,    -17.18,     13.82)
   Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
   Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:15:09_2016_modification_3.pdb.gz
INFO:: Command: (setnum-from-serial-number 147 "B" 0)
INFO:: Command: (setnum-from-serial-number 147 "B" 1)
INFO:: Command: (setnum-from-serial-number 147 "B" 2)
INFO:: Command: (setnum-from-serial-number 147 "B" 3)
INFO:: Command: (setnum-from-serial-number 147 "B" 4)
INFO:: Command: (setnum-from-serial-number 147 "B" 5)
INFO:: Command: (setnum-from-serial-number 147 "B" 6)
INFO:: Command: (setnum-from-serial-number 147 "B" 7)
INFO:: Command: (setnum-from-serial-number 147 "B" 8)
INFO:: Command: (setnum-from-serial-number 147 "B" 9)
INFO:: Command: (setnum-from-serial-number 147 "B" 10)
INFO:: Command: (setnum-from-serial-number 147 "B" 11)
INFO:: Command: (setnum-from-serial-number 147 "B" 12)
INFO:: Command: (setnum-from-serial-number 147 "B" 13)
INFO:: Command: (setnum-from-serial-number 147 "B" 14)
INFO:: Command: (setnum-from-serial-number 147 "B" 15)
INFO:: Command: (setnum-from-serial-number 147 "B" 16)
INFO:: Command: (setnum-from-serial-number 147 "B" 17)
INFO:: Command: (setnum-from-serial-number 147 "B" 18)
INFO:: Command: (setnum-from-serial-number 147 "B" 19)
INFO:: Command: (setnum-from-serial-number 147 "B" 20)
INFO:: Command: (setnum-from-serial-number 147 "B" 21)
INFO:: Command: (setnum-from-serial-number 147 "B" 22)
INFO:: Command: (setnum-from-serial-number 147 "B" 23)
INFO:: Command: (setnum-from-serial-number 147 "B" 24)
INFO:: Command: (setnum-from-serial-number 147 "B" 25)
INFO:: Command: (setnum-from-serial-number 147 "B" 26)
INFO:: Command: (setnum-from-serial-number 147 "B" 27)
INFO:: Command: (setnum-from-serial-number 147 "B" 28)
INFO:: Command: (setnum-from-serial-number 147 "B" 29)
INFO:: Command: (setnum-from-serial-number 147 "B" 30)
INFO:: Command: (setnum-from-serial-number 147 "B" 31)
INFO:: Command: (setnum-from-serial-number 147 "B" 32)
INFO:: Command: (setnum-from-serial-number 147 "B" 33)
INFO:: Command: (setnum-from-serial-number 147 "B" 34)
INFO:: Command: (setnum-from-serial-number 147 "B" 35)
INFO:: Command: (setnum-from-serial-number 147 "B" 36)
INFO:: Command: (setnum-from-serial-number 147 "B" 37)
INFO:: Command: (setnum-from-serial-number 147 "B" 38)
INFO:: Command: (setnum-from-serial-number 147 "B" 39)
INFO:: Command: (setnum-from-serial-number 147 "B" 40)
INFO:: Command: (setnum-from-serial-number 147 "B" 41)
INFO:: Command: (setnum-from-serial-number 147 "B" 42)
INFO:: Command: (setnum-from-serial-number 147 "B" 43)
INFO:: Command: (setnum-from-serial-number 147 "B" 44)
INFO:: Command: (setnum-from-serial-number 147 "B" 45)
INFO:: Command: (setnum-from-serial-number 147 "B" 46)
INFO:: Command: (setnum-from-serial-number 147 "B" 47)
INFO:: Command: (setnum-from-serial-number 147 "B" 48)
INFO:: Command: (setnum-from-serial-number 147 "B" 49)
INFO:: Command: (setnum-from-serial-number 147 "B" 50)
INFO:: Command: (setnum-from-serial-number 147 "B" 51)
INFO:: Command: (setnum-from-serial-number 147 "B" 52)
INFO:: Command: (setnum-from-serial-number 147 "B" 53)
INFO:: Command: (setnum-from-serial-number 147 "B" 54)
INFO:: Command: (setnum-from-serial-number 147 "B" 55)
INFO:: Command: (setnum-from-serial-number 147 "B" 56)
INFO:: Command: (setnum-from-serial-number 147 "B" 57)
INFO:: Command: (setnum-from-serial-number 147 "B" 58)
INFO:: Command: (setnum-from-serial-number 147 "B" 59)
INFO:: Command: (setnum-from-serial-number 147 "B" 60)
INFO:: Command: (setnum-from-serial-number 147 "B" 61)
INFO:: Command: (setnum-from-serial-number 147 "B" 62)
INFO:: Command: (setnum-from-serial-number 147 "B" 63)
INFO:: Command: (setnum-from-serial-number 147 "B" 64)
INFO:: Command: (setnum-from-serial-number 147 "B" 65)
INFO:: Command: (setnum-from-serial-number 147 "B" 66)
INFO:: Command: (setnum-from-serial-number 147 "B" 67)
INFO:: Command: (setnum-from-serial-number 147 "B" 68)
INFO:: Command: (setnum-from-serial-number 147 "B" 69)
INFO:: Command: (setnum-from-serial-number 147 "B" 70)
INFO:: Command: (setnum-from-serial-number 147 "B" 71)
INFO:: Command: (setnum-from-serial-number 147 "B" 72)
INFO:: Command: (setnum-from-serial-number 147 "B" 73)
INFO:: Command: (setnum-from-serial-number 147 "B" 74)
INFO:: Command: (setnum-from-serial-number 147 "B" 75)
INFO:: Command: (setnum-from-serial-number 147 "B" 76)
INFO:: Command: (setnum-from-serial-number 147 "B" 77)
INFO:: Command: (setnum-from-serial-number 147 "B" 78)
INFO:: Command: (setnum-from-serial-number 147 "B" 79)
INFO:: Command: (setnum-from-serial-number 147 "B" 80)
INFO:: Command: (setnum-from-serial-number 147 "B" 81)
INFO:: Command: (setnum-from-serial-number 147 "B" 82)
INFO:: Command: (setnum-from-serial-number 147 "B" 83)
INFO:: Command: (setnum-from-serial-number 147 "B" 84)
INFO:: Command: (setnum-from-serial-number 147 "B" 85)
INFO:: Command: (setnum-from-serial-number 147 "B" 86)
INFO:: Command: (setnum-from-serial-number 147 "B" 87)
INFO:: Command: (setnum-from-serial-number 147 "B" 88)
INFO:: Command: (setnum-from-serial-number 147 "B" 89)
INFO:: Command: (setnum-from-serial-number 147 "B" 90)
INFO:: Command: (setnum-from-serial-number 147 "B" 91)
INFO:: Command: (setnum-from-serial-number 147 "B" 92)
INFO:: Command: (setnum-from-serial-number 147 "B" 93)
INFO:: Command: (setnum-from-serial-number 147 "B" 94)
INFO:: Command: (setnum-from-serial-number 147 "B" 95)
INFO:: mutate 2 A to a TRP
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:15:09_2016_modification_4.pdb.gz
INFO:: Command: (mutate 147 "A" 2 "" "TRP")
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 147 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 147 and ichain: 0
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 0
   Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 92/93
First atom of 727 in first  selection 1/A/1 {ASP}/ N   altLoc :: segid :: pos: (44.8780,12.9550,8.7610) B-factor: 30.1700
First atom of 745 in second selection 1/B/1 {ASP}/ N   altLoc :: segid :: pos: (13.7154,16.0316,23.2057) B-factor: 30.1700
INFO:: LSQ matched 93 atoms
INFO:: 93 matched atoms had: 
   mean devi: 0.3427
    rms devi: 0.4454
    max devi: 2.1352
    min devi: 0.0124
   find_ncs_matrix returns (LSQ) 
|    0.9705,  -0.04643,   -0.2365|
|    0.2356,    0.3891,    0.8906|
|   0.05068,     -0.92,    0.3886|
(      37.8,    -17.17,     13.81)
   Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: set_ncs_master_chain Constructed 1 ghosts
   Ghost info:: NCS found from matching Chain B onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Tue_Dec_27_04:15:09_2016_modification_5.pdb.gz
ok
test05_0 (__main__.NcsTestFunctions)
NCS Residue Range edit to all chains ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1t6q.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1t6q.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1t6q.ent has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 110/110
INFO:: NCS chain comparison 110/110
  INFO:: fill_ghost_info Constructed 2 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Molecule 148 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: mutate 50 A to a ASP
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Dec_27_04:15:10_2016_modification_0.pdb.gz
INFO:: Command: (mutate 148 "A" 50 "" "ASP")
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"
INFO:: Command: (is-solvent-chain-p 148 "B")
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 148 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 148 and ichain: 0
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 0
   Checking chains for NCS matching to chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first  selection 1/A/7 {GLY}/ N   altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 893 in second selection 1/B/6 {CYS}/ N   altLoc :: segid :: pos: (45.3620,34.2400,30.6710) B-factor: 84.3600
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had: 
   mean devi: 0.2048
    rms devi: 0.2651
    max devi: 1.1707
    min devi: 0.0160
   find_ncs_matrix returns (LSQ) 
|    0.5407,    0.4775,    0.6926|
|   -0.4862,   -0.4944,    0.7205|
|    0.6865,   -0.7263,  -0.03511|
(    -28.15,     65.89,      42.9)
   Adding ghost with name: NCS found from matching Chain B onto Chain A
INFO:: NCS chain comparison 109/110
First atom of 881 in first  selection 1/A/7 {GLY}/ N   altLoc :: segid :: pos: (31.7950,49.9730,50.8660) B-factor: 68.1800
First atom of 881 in second selection 1/C/7 {GLY}/ N   altLoc :: segid :: pos: (47.6640,58.9920,25.9960) B-factor: 67.7200
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had: 
   mean devi: 0.2275
    rms devi: 0.3035
    max devi: 1.6549
    min devi: 0.0661
   find_ncs_matrix returns (LSQ) 
|    0.5303,   -0.4851,    0.6953|
|    0.4758,   -0.5085,   -0.7177|
|    0.7017,    0.7114,  -0.03884|
(     18.19,     77.78,    -25.69)
   Adding ghost with name: NCS found from matching Chain C onto Chain A
INFO:: set_ncs_master_chain Constructed 2 ghosts
   Ghost info:: NCS found from matching Chain B onto Chain A
   Ghost info:: NCS found from matching Chain C onto Chain A
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Dec_27_04:15:10_2016_modification_1.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Tue_Dec_27_04:15:10_2016_modification_2.pdb.gz
result: [True, True]
ok
test06_0 (__main__.NcsTestFunctions)
Manual NCS ghosts generates correct NCS chain ids ... INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 149 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 149 and chain_id: B
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 1
   Checking chains for NCS matching to chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first  selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 540 in second selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.4989
    rms devi: 2.7962
    max devi: 6.6860
    min devi: 0.4401
   find_ncs_matrix returns (LSQ) 
|    0.7026,    0.1278,       0.7|
|    0.6024,    0.4169,   -0.6807|
|   -0.3788,    0.8999,    0.2159|
(     62.25,    -87.53,    -9.128)
   Adding ghost with name: NCS found from matching Chain A onto Chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first  selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 535 in second selection 1/C/190 {GLN}/ N   altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.6728
    rms devi: 2.9369
    max devi: 6.1200
    min devi: 0.2483
   find_ncs_matrix returns (LSQ) 
|   -0.3504,   -0.8022,   -0.4834|
|   -0.7587,  -0.05952,    0.6488|
|   -0.5492,     0.594,   -0.5878|
(    -29.05,     14.61,    -72.53)
   Adding ghost with name: NCS found from matching Chain C onto Chain B
INFO:: NCS chain comparison 61/62
First atom of 506 in first  selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 497 in second selection 1/D/193 {SER}/ N   altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had: 
   mean devi: 1.7317
    rms devi: 1.9769
    max devi: 7.9453
    min devi: 0.5297
   find_ncs_matrix returns (LSQ) 
|   -0.3815,   -0.9208,  -0.08098|
|   -0.9191,    0.3685,    0.1396|
|  -0.09874,    0.1277,   -0.9869|
(    -11.18,     4.757,    -127.2)
   Adding ghost with name: NCS found from matching Chain D onto Chain B
INFO:: NCS chain comparison 0/62
INFO:: set_ncs_master_chain Constructed 3 ghosts
   Ghost info:: NCS found from matching Chain A onto Chain B
   Ghost info:: NCS found from matching Chain C onto Chain B
   Ghost info:: NCS found from matching Chain D onto Chain B
Symmetry available for this molecule
INFO:: Command: (copy-molecule 149)
INFO:: Matching/moving molecule number 150 to 149
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had: 
   mean devi: 0.2239
    rms devi: 0.2350
    max devi: 0.3369
    min devi: 0.0588
INFO:: Axis orientation: (    0.7368,    0.6481,    0.1925)
INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Dec_27_04:15:12_2016_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)
chain_id A master B rtop: [[0.3394591924816796, 0.5177117455596953, 0.7853292336015637, 0.8624279581117553, 0.16197572619124062, -0.4795642617960695, -0.3754803239943135, 0.8400823844328328, -0.39150493439900846], [90.55110034747929, -91.12318261711249, -47.52179998745863]]
INFO:: Matching/moving molecule number 150 to 149
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: (    0.1978,   -0.3281,    0.9237)
INFO:: Rotation in CCP4 Polar Angles: Polar = (22.5246,-58.9204,174.877)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Dec_27_04:15:12_2016_modification_1.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|   -0.9179,    -0.212,    0.3353|
|  -0.04702,   -0.7812,   -0.6226|
|    0.3939,   -0.5873,    0.7071|
(      57.6,    -116.4,    -53.95)
INFO:: fractional coordinates matrix:
|   -0.9451,   -0.1016,  -0.03159|
|  -0.05429,    -0.754,   -0.9411|
|    0.3009,   -0.5389,    0.7071|
(    -0.109,    -1.522,   -0.4666)
chain_id C master B rtop: [[-0.9179458350933407, -0.21199297393104302, 0.33531242571467806, -0.04701514428682865, -0.7811500284294697, -0.6225706460252742, 0.39390991361284383, -0.5872508936464131, 0.7070865349227144], [57.59590387868751, -116.43599115338534, -53.953192756327674]]
INFO:: Matching/moving molecule number 150 to 149
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: (    0.7055,    0.6938,    0.1447)
INFO:: Rotation in CCP4 Polar Angles: Polar = (98.3189,-135.478,101.097)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_pdb1hvv.ent_Tue_Dec_27_04:15:12_2016_modification_2.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|     0.401,    0.7256,   -0.5591|
|    0.4417,    0.3815,     0.812|
|    0.8025,   -0.5726,   -0.1675|
(     8.426,     15.74,    -123.4)
INFO:: fractional coordinates matrix:
|     0.656,    0.4912,   -0.1182|
|      0.51,    0.1265,     1.227|
|    0.6131,   -0.6853,   -0.1675|
(    0.1983,    0.2058,    -1.067)
chain_id D master B rtop: [[0.4010296958260637, 0.7256475124974693, -0.5591161513244722, 0.44169126456601965, 0.38154476969746226, 0.8119928666697639, 0.8025484470558306, -0.5725899722513011, -0.16750138448839502], [8.42628578842055, 15.739925910905619, -123.41057067974724]]
INFO:: Command: (close-molecule 150)
   NCS ghost chain IDs pre:   [['B', 'A', 'C', 'D']]
   NCS ghost chain IDs post:  [['B', 'A', 'C', 'D']]
ok
test07_0 (__main__.NcsTestFunctions)
NCS maps overwrite existing maps ... INFO:: Command: (molecule-name 0)
INFO:: Command: (molecule-name 1)
INFO:: Command: (molecule-name 4)
INFO:: Command: (molecule-name 5)
INFO:: Command: (molecule-name 6)
INFO:: Command: (molecule-name 7)
INFO:: Command: (molecule-name 8)
INFO:: Command: (molecule-name 9)
INFO:: Command: (molecule-name 10)
INFO:: Command: (molecule-name 11)
INFO:: Command: (molecule-name 13)
INFO:: Command: (molecule-name 14)
INFO:: Command: (molecule-name 15)
INFO:: Command: (molecule-name 17)
INFO:: Command: (molecule-name 18)
INFO:: Command: (molecule-name 21)
INFO:: Command: (molecule-name 22)
INFO:: Command: (molecule-name 23)
INFO:: Command: (molecule-name 25)
INFO:: Command: (molecule-name 26)
INFO:: Command: (molecule-name 28)
INFO:: Command: (molecule-name 29)
INFO:: Command: (molecule-name 30)
INFO:: Command: (molecule-name 32)
INFO:: Command: (molecule-name 33)
INFO:: Command: (molecule-name 34)
INFO:: Command: (molecule-name 35)
INFO:: Command: (molecule-name 36)
INFO:: Command: (molecule-name 39)
INFO:: Command: (molecule-name 48)
INFO:: Command: (molecule-name 49)
INFO:: Command: (molecule-name 51)
INFO:: Command: (molecule-name 52)
INFO:: Command: (molecule-name 53)
INFO:: Command: (molecule-name 54)
INFO:: Command: (molecule-name 55)
INFO:: Command: (molecule-name 56)
INFO:: Command: (molecule-name 57)
INFO:: Command: (molecule-name 58)
INFO:: Command: (molecule-name 59)
INFO:: Command: (molecule-name 60)
INFO:: Command: (molecule-name 61)
INFO:: Command: (molecule-name 62)
INFO:: Command: (molecule-name 63)
INFO:: Command: (molecule-name 65)
INFO:: Command: (molecule-name 66)
INFO:: Command: (molecule-name 67)
INFO:: Command: (molecule-name 68)
INFO:: Command: (molecule-name 69)
INFO:: Command: (molecule-name 70)
INFO:: Command: (molecule-name 71)
INFO:: Command: (molecule-name 72)
INFO:: Command: (molecule-name 73)
INFO:: Command: (molecule-name 74)
INFO:: Command: (molecule-name 75)
INFO:: Command: (molecule-name 77)
INFO:: Command: (molecule-name 78)
INFO:: Command: (molecule-name 79)
INFO:: Command: (molecule-name 80)
INFO:: Command: (molecule-name 81)
INFO:: Command: (molecule-name 82)
INFO:: Command: (molecule-name 83)
INFO:: Command: (molecule-name 84)
INFO:: Command: (molecule-name 85)
INFO:: Command: (molecule-name 86)
INFO:: Command: (molecule-name 87)
INFO:: Command: (molecule-name 88)
INFO:: Command: (molecule-name 89)
INFO:: Command: (molecule-name 90)
INFO:: Command: (molecule-name 91)
INFO:: Command: (molecule-name 92)
INFO:: Command: (molecule-name 93)
INFO:: Command: (molecule-name 97)
INFO:: Command: (molecule-name 98)
INFO:: Command: (molecule-name 100)
INFO:: Command: (molecule-name 101)
INFO:: Command: (molecule-name 102)
INFO:: Command: (molecule-name 103)
INFO:: Command: (molecule-name 104)
INFO:: Command: (molecule-name 105)
INFO:: Command: (molecule-name 106)
INFO:: Command: (molecule-name 107)
INFO:: Command: (molecule-name 108)
INFO:: Command: (molecule-name 109)
INFO:: Command: (molecule-name 110)
INFO:: Command: (molecule-name 111)
INFO:: Command: (molecule-name 112)
INFO:: Command: (molecule-name 113)
INFO:: Command: (molecule-name 114)
INFO:: Command: (molecule-name 118)
INFO:: Command: (molecule-name 119)
INFO:: Command: (molecule-name 120)
INFO:: Command: (molecule-name 121)
INFO:: Command: (molecule-name 122)
INFO:: Command: (molecule-name 123)
INFO:: Command: (molecule-name 124)
INFO:: Command: (molecule-name 125)
INFO:: Command: (molecule-name 126)
INFO:: Command: (molecule-name 127)
INFO:: Command: (molecule-name 128)
INFO:: Command: (molecule-name 129)
INFO:: Command: (molecule-name 130)
INFO:: Command: (molecule-name 131)
INFO:: Command: (molecule-name 132)
INFO:: Command: (molecule-name 134)
INFO:: Command: (molecule-name 135)
INFO:: Command: (molecule-name 136)
INFO:: Command: (molecule-name 137)
INFO:: Command: (molecule-name 138)
INFO:: Command: (molecule-name 139)
INFO:: Command: (molecule-name 140)
INFO:: Command: (close-molecule 142)
INFO:: Command: (close-molecule 144)
INFO:: Command: (molecule-name 146)
INFO:: Command: (molecule-name 147)
INFO:: Command: (molecule-name 148)
INFO:: Command: (molecule-name 149)
INFO:: Command: (handle-read-draw-molecule-with-recentre "/lmb/home/pemsley/data/greg-data/pdb1hvv.ent" 1)
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
 PDB file /lmb/home/pemsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 151 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (make-and-draw-map "/lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0)
INFO:: making map from mtz filename /lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz
Number of OBSERVED reflections: 20903
INFO:: finding ASU unique map points with sampling rate 1.5000
INFO grid sampling...Nuvw = ( 112, 112, 150)
INFO:: 0.0650 seconds to read MTZ file
INFO:: 0.0340 seconds to initialize map
INFO:: 0.0450 seconds for FFT
INFO:: 0.0070 seconds for statistics
      Map mean: ........ -0.0000
      Map sigma: ....... 0.2241
      Map maximum: ..... 1.7219
      Map minimum: ..... -0.8818
INFO:: 0.0110 seconds for contour map
INFO:: 0.1620 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 152 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 152 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 152 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 152 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 152 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 152 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 152 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 152 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 152 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:: Command: (molecule-name 0)
INFO:: Command: (molecule-name 1)
INFO:: Command: (molecule-name 4)
INFO:: Command: (molecule-name 5)
INFO:: Command: (molecule-name 6)
INFO:: Command: (molecule-name 7)
INFO:: Command: (molecule-name 8)
INFO:: Command: (molecule-name 9)
INFO:: Command: (molecule-name 10)
INFO:: Command: (molecule-name 11)
INFO:: Command: (molecule-name 13)
INFO:: Command: (molecule-name 14)
INFO:: Command: (molecule-name 15)
INFO:: Command: (molecule-name 17)
INFO:: Command: (molecule-name 18)
INFO:: Command: (molecule-name 21)
INFO:: Command: (molecule-name 22)
INFO:: Command: (molecule-name 23)
INFO:: Command: (molecule-name 25)
INFO:: Command: (molecule-name 26)
INFO:: Command: (molecule-name 28)
INFO:: Command: (molecule-name 29)
INFO:: Command: (molecule-name 30)
INFO:: Command: (molecule-name 32)
INFO:: Command: (molecule-name 33)
INFO:: Command: (molecule-name 34)
INFO:: Command: (molecule-name 35)
INFO:: Command: (molecule-name 36)
INFO:: Command: (molecule-name 39)
INFO:: Command: (molecule-name 48)
INFO:: Command: (molecule-name 49)
INFO:: Command: (molecule-name 51)
INFO:: Command: (molecule-name 52)
INFO:: Command: (molecule-name 53)
INFO:: Command: (molecule-name 54)
INFO:: Command: (molecule-name 55)
INFO:: Command: (molecule-name 56)
INFO:: Command: (molecule-name 57)
INFO:: Command: (molecule-name 58)
INFO:: Command: (molecule-name 59)
INFO:: Command: (molecule-name 60)
INFO:: Command: (molecule-name 61)
INFO:: Command: (molecule-name 62)
INFO:: Command: (molecule-name 63)
INFO:: Command: (molecule-name 65)
INFO:: Command: (molecule-name 66)
INFO:: Command: (molecule-name 67)
INFO:: Command: (molecule-name 68)
INFO:: Command: (molecule-name 69)
INFO:: Command: (molecule-name 70)
INFO:: Command: (molecule-name 71)
INFO:: Command: (molecule-name 72)
INFO:: Command: (molecule-name 73)
INFO:: Command: (molecule-name 74)
INFO:: Command: (molecule-name 75)
INFO:: Command: (molecule-name 77)
INFO:: Command: (molecule-name 78)
INFO:: Command: (molecule-name 79)
INFO:: Command: (molecule-name 80)
INFO:: Command: (molecule-name 81)
INFO:: Command: (molecule-name 82)
INFO:: Command: (molecule-name 83)
INFO:: Command: (molecule-name 84)
INFO:: Command: (molecule-name 85)
INFO:: Command: (molecule-name 86)
INFO:: Command: (molecule-name 87)
INFO:: Command: (molecule-name 88)
INFO:: Command: (molecule-name 89)
INFO:: Command: (molecule-name 90)
INFO:: Command: (molecule-name 91)
INFO:: Command: (molecule-name 92)
INFO:: Command: (molecule-name 93)
INFO:: Command: (molecule-name 97)
INFO:: Command: (molecule-name 98)
INFO:: Command: (molecule-name 100)
INFO:: Command: (molecule-name 101)
INFO:: Command: (molecule-name 102)
INFO:: Command: (molecule-name 103)
INFO:: Command: (molecule-name 104)
INFO:: Command: (molecule-name 105)
INFO:: Command: (molecule-name 106)
INFO:: Command: (molecule-name 107)
INFO:: Command: (molecule-name 108)
INFO:: Command: (molecule-name 109)
INFO:: Command: (molecule-name 110)
INFO:: Command: (molecule-name 111)
INFO:: Command: (molecule-name 112)
INFO:: Command: (molecule-name 113)
INFO:: Command: (molecule-name 114)
INFO:: Command: (molecule-name 118)
INFO:: Command: (molecule-name 119)
INFO:: Command: (molecule-name 120)
INFO:: Command: (molecule-name 121)
INFO:: Command: (molecule-name 122)
INFO:: Command: (molecule-name 123)
INFO:: Command: (molecule-name 124)
INFO:: Command: (molecule-name 125)
INFO:: Command: (molecule-name 126)
INFO:: Command: (molecule-name 127)
INFO:: Command: (molecule-name 128)
INFO:: Command: (molecule-name 129)
INFO:: Command: (molecule-name 130)
INFO:: Command: (molecule-name 131)
INFO:: Command: (molecule-name 132)
INFO:: Command: (molecule-name 134)
INFO:: Command: (molecule-name 135)
INFO:: Command: (molecule-name 136)
INFO:: Command: (molecule-name 137)
INFO:: Command: (molecule-name 138)
INFO:: Command: (molecule-name 139)
INFO:: Command: (molecule-name 140)
INFO:: Command: (molecule-name 146)
INFO:: Command: (molecule-name 147)
INFO:: Command: (molecule-name 148)
INFO:: Command: (molecule-name 149)
INFO:: Command: (molecule-name 151)
BL DEBUG:: molecule_names ['/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/ins-code-fragment-pre.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'mainchain', '/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb', 'regression-test-terminal-residue.pdb', 'atom selection from regression-test-terminal-residue.pdb', '/lmb/home/pemsley/data/greg-data/frag-2wot.pdb', 'sphere selection from tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rotamer-test-fragment.pdb', '/lmb/home/pemsley/data/greg-data/res098.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/pdb3knw.ent', '/lmb/home/pemsley/data/greg-data/pdb1py3.ent', '/lmb/home/pemsley/data/greg-data/alt-conf-pepflip-test.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/tutorial-add-terminal-1-test.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/alt-conf-waters.pdb', '/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/backrub-fragment.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT', '/lmb/home/pemsley/data/greg-data/test-TER-OXT.pdb', '/lmb/home/pemsley/data/greg-data/val.pdb', '/lmb/home/pemsley/data/greg-data/2yie-frag.pdb', '/lmb/home/pemsley/data/greg-data/4f8g.pdb', '/lmb/home/pemsley/data/greg-data/4f8g.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'Generic Masked Map', 'difference-map', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'averaged-map', 'difference-map', '/lmb/home/pemsley/data/greg-data/multi-carbo-coot-2.pdb', '/lmb/home/pemsley/data/greg-data/pdb2qc1-sans-cho.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/monomer-VAL.pdb', '/lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb', 'atom selection from tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'atom selection from tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnase-A-needs-an-insertion.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb3hfl.ent', '/lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Ideal-A-form-RNA', 'Ideal-A-form-RNA', 'Ideal-A-form-DNA', 'Ideal-A-form-DNA', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb', '/lmb/home/pemsley/data/greg-data/tm+some-waters.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb', '/lmb/home/pemsley/data/greg-data/pathological-water-test.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb1hvv.ent', '/lmb/home/pemsley/data/greg-data/monomer-ACT.pdb', '/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'SymOp_-X,-X+Y,-Z+1/3_Copy_of_79', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb1py3.ent', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/2goz-manip.pdb', 'rnase_zip_test.pdb.gz', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/HOF.RES', '/lmb/home/pemsley/data/greg-data/hollander.ins', '/lmb/home/pemsley/data/greg-data/insulin.fcf Diff-SigmaA', 'atom selection from insulin.res', 'atom selection from insulin.res', '/lmb/home/pemsley/data/greg-data/horma-p21.res', 'new-horma.ins', '/lmb/home/pemsley/data/greg-data/crash.hat', '/lmb/home/pemsley/data/greg-data/crash.hat', 'coot-ccp4/monomer-3GP.pdb', '/lmb/home/pemsley/data/greg-data/monomer-3GP.pdb', '/lmb/home/pemsley/data/greg-data/test-LIG.pdb', '/lmb/home/pemsley/data/greg-data/test-LIG.pdb', '/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', 'Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb', '/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb', '/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT', '/lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT', 'Masked (by protein)', 'Fitted ligand #0-0', 'Fitted ligand #1-0', 'Fitted ligand #2-0', 'Fitted ligand #3-0', 'Fitted ligand #4-0', 'Fitted ligand #5-0', 'Fitted ligand #6-0', 'Fitted ligand #7-0', 'Fitted ligand #8-0', 'Fitted ligand #9-0', 'coot-ccp4/monomer-3GP.pdb', 'Copy_of_coot-ccp4/monomer-3GP.pdb', '/lmb/home/pemsley/data/greg-data/dipole-residues.pdb', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', 'Copy_of_Ideal-A-form-RNA', '/lmb/home/pemsley/data/greg-data/1wly.pdb', '/lmb/home/pemsley/data/greg-data/1yb5.pdb', '/lmb/home/pemsley/data/greg-data/2qd9.pdb', '/lmb/home/pemsley/data/greg-data/2gtn.pdb', '/lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT', 'Map 2 NCS average of Chain A type molecules', 'Map 141 NCS average of Chain A type molecules', '/lmb/home/pemsley/data/greg-data/insulin.res', '/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb', '/lmb/home/pemsley/data/greg-data/pdb1t6q.ent', '/lmb/home/pemsley/data/greg-data/pdb1hvv.ent', '/lmb/home/pemsley/data/greg-data/pdb1hvv.ent', '/lmb/home/pemsley/data/greg-data/1hvv_sigmaa.mtz 2FOFCWT PH2FOFCWT', 'Map 152 NCS found from matching Chain B onto Chain A', 'Map 152 NCS found from matching Chain C onto Chain A', 'Map 152 NCS found from matching Chain D onto Chain A', 'Map 152 NCS average of Chain A type molecules', 'Map 152 NCS found from matching Chain B onto Chain A', 'Map 152 NCS found from matching Chain C onto Chain A', 'Map 152 NCS found from matching Chain D onto Chain A', 'Map 152 NCS average of Chain A type molecules']
BL DEBUG:: n_matchers 2
BL DEBUG:: n_matchers 2
BL DEBUG:: n_matchers 2
ok
test01_0 (__main__.UtilTestFunctions)
Test key symbols ... ok
test02_0 (__main__.UtilTestFunctions)
Test running a scheme function ... INFO:: Command: (+ 2 4)
INFO:: Command: (rotation-centre)
INFO:: Command: (rotation-centre-position 0)
INFO:: Command: (rotation-centre-position 1)
INFO:: Command: (rotation-centre-position 2)
BL DEBUG:: return scheme is  [24.219083786010742, -41.04264831542969, -67.95923614501953]
INFO:: Command: 2
ok
test03_0 (__main__.UtilTestFunctions)
Internal/External Molecule Numbers match ... ok
test05_0 (__main__.UtilTestFunctions)
Import gobject ... ok
test_00 (__main__.InternalTestFunctions)
Test internal functions ... Entering test: kevin's torsion test
PASS: kevin's torsion test
Entering test: test_alt_conf_rotamers
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
PASS: test_alt_conf_rotamers
Entering test: test_fragmemt_atom_selection
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
   n_initial: 1465   n_1: 1401   n_2: 64
PASS: test_fragmemt_atom_selection
Entering test: test_add_atom
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
PASS: test_add_atom
Entering test: test dictionary partial charges
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/
There are 142 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ALA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ASN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLN.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLY.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GLU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PHE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HIS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/i/ILE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LYS.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/l/LEU.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MET.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/m/MSE.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PRO.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/ARG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SER.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/THR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/v/VAL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TRP.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/t/TYR.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/p/PO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/s/SO4.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/GOL.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/CIT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/a/A.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/c/C.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/g/G.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/u/U.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DA.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DC.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DG.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/d/DT.cif
There are 2 data in /lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/h/HOH.cif
PASS: test dictionary partial charges
Entering test: test segid exchange
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
   Test with a rogue segid 
   INFO:: No consistent segids for residue 1
PASS: test segid exchange
Entering test: test ligand from point
There are 2 data in /lmb/home/pemsley/data/greg-data/libcheck_3GP-torsion-filtered.cif
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
 PDB file /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
reading mtz file...
Number of reflections: 17982
finding ASU unique map points...
Grid...Nuvw = ( 108, 132,  64)
doing fft...
done fft...
get_monomer type: 3GP
This residue has 25 defined non-H torsions of which 6 are (non-const) rotatable and 6 are non-const and non-ring torsions
 non-H torsion:   0 [torsion-restraint: CONST_1  O6   C6   C5   N7  0.0000 0.0000 0 CONST ]
 non-H torsion:   1 [torsion-restraint: CONST_2  C6   C5   C4   N3  0.0000 0.0000 0 CONST ]
 non-H torsion:   2 [torsion-restraint: CONST_3  C6   C5   C4   N9  180.0000 0.0000 0 CONST ]
 non-H torsion:   3 [torsion-restraint: CONST_4  C5   C4   N3   C2  0.0000 0.0000 0 CONST ]
 non-H torsion:   4 [torsion-restraint: CONST_5  C4   N3   C2   N1  0.0000 0.0000 0 CONST ]
 non-H torsion:   5 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1]
 non-H torsion:   6 [torsion-restraint: CONST_6  N3   C2   N1   C6  0.0000 0.0000 0 CONST ]
 non-H torsion:   7 [torsion-restraint: CONST_12  N3   C2   N1   HN1 180.0000 0.0000 0 CONST ]
 non-H torsion:   8 [torsion-restraint: CONST_7  C6   C5   N7   C8  180.0000 0.0000 0 CONST ]
 non-H torsion:   9 [torsion-restraint: CONST_8  C5   N7   C8   N9  0.0000 0.0000 0 CONST ]
 non-H torsion:   10 [torsion-restraint: CONST_9  N7   C8   N9   C1* 180.0000 0.0000 0 CONST ]
 non-H torsion:   11 [torsion-restraint: CONST_10  N7   C8   N9   C4  0.0000 0.0000 0 CONST ]
 non-H torsion:   12 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1]
 non-H torsion:   13 [torsion-restraint: CONST_var_3  N9   C1*  O4*  C4* -152.9040 20.0000 1 CONST ]
 non-H torsion:   14 [torsion-restraint: CONST_var_4  C1*  O4*  C4*  C5* 124.2120 20.0000 1 CONST ]
 non-H torsion:   15 [torsion-restraint: CONST_var_5  C1*  O4*  C4*  C3* -3.5110 20.0000 1 CONST ]
 non-H torsion:   16 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3]
 non-H torsion:   17 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1]
 non-H torsion:   18 [torsion-restraint: CONST_var_8  N9   C1*  C2*  C3* 155.4840 20.0000 3 CONST ]
 non-H torsion:   19 [torsion-restraint: CONST_var_9  C1*  C2*  O2* HO2* 0.0000 20.0000 1 CONST ]
 non-H torsion:   20 [torsion-restraint: CONST_var_10  C1*  C2*  C3*  O3* 82.0740 20.0000 3 CONST ]
 non-H torsion:   21 [torsion-restraint: CONST_11  C1*  C2*  C3*  H3* -157.9260 0.0000 0 CONST ]
 non-H torsion:   22 [torsion-restraint: CONST_var_11  C1*  C2*  C3*  C4* -36.8410 20.0000 3 CONST ]
 non-H torsion:   23 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1]
 non-H torsion:   24 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1]
 non-H-non-ring-non-const torsion:   0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1]
 non-H-non-ring-non-const torsion:   1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1]
 non-H-non-ring-non-const torsion:   2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3]
 non-H-non-ring-non-const torsion:   3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1]
 non-H-non-ring-non-const torsion:   4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1]
 non-H-non-ring-non-const torsion:   5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1]
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] -37.7990
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -77.9788
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 17.9613
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] -42.7765
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -189.6486
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -165.3342
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 4 chiral vol restraints 
created 109 restraints

INFO:: make_restraints(): made 382 non-bonded restraints
initial distortion_score: 39.2650
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.0706
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 886) at 10.7476
    Final Estimated RMS Z Scores:
bonds:      0.0836
angles:     0.3967
torsions:   N/A 
planes:     0.0030
non-bonded: 0.0002
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
INFO:: setup minimol from mol: no spacegroup
ligand eigen values: 26.1517  96.3565  422.0211  
 ligand eigen vectors: 
|   -0.1273,    0.2063,   -0.9702|
|   -0.3107,    0.9206,    0.2365|
|     0.942,    0.3315,  -0.05314|
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] -16.3525
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -102.7152
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 141.2318
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] 5.0162
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -165.0437
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -178.1232
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 4 chiral vol restraints 
created 109 restraints

INFO:: make_restraints(): made 384 non-bonded restraints
initial distortion_score: 22.9869
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.0278
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
INFO:: setup minimol from mol: no spacegroup
ligand eigen values: 18.7250  94.5292  426.7002  
 ligand eigen vectors: 
|     -0.12,      0.17,   -0.9781|
|  -0.07093,    0.9813,    0.1792|
|    0.9902,   0.09088,   -0.1057|
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] -33.6781
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -77.0000
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 203.7947
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] 5.7956
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -192.2903
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -164.8237
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 4 chiral vol restraints 
created 109 restraints

INFO:: make_restraints(): made 378 non-bonded restraints
initial distortion_score: 217.4272
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.5427
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
INFO:: setup minimol from mol: no spacegroup
ligand eigen values: 23.8252  86.5007  440.5973  
 ligand eigen vectors: 
|   -0.1326,    0.2049,   -0.9698|
|   -0.2499,    0.9399,    0.2328|
|    0.9591,    0.2732,  -0.07346|
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] -17.7051
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -78.2935
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 27.4747
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] -36.7856
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -189.8637
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -149.9372
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 4 chiral vol restraints 
created 109 restraints

INFO:: make_restraints(): made 381 non-bonded restraints
initial distortion_score: 26.2928
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.0367
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 758) at 10.7519
    Final Estimated RMS Z Scores:
bonds:      0.0835
angles:     0.3968
torsions:   N/A 
planes:     0.0043
non-bonded: 0.0002
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
INFO:: setup minimol from mol: no spacegroup
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] -5.7646
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -50.3272
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 54.0833
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] -3.6138
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -163.0316
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -160.0986
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 4 chiral vol restraints 
created 109 restraints

INFO:: make_restraints(): made 385 non-bonded restraints
initial distortion_score: 26.9340
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.0380
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 967) at 10.7497
    Final Estimated RMS Z Scores:
bonds:      0.0833
angles:     0.3968
torsions:   N/A 
planes:     0.0026
non-bonded: 0.0002
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
INFO:: setup minimol from mol: no spacegroup
ligand eigen values: 46.1699  75.0365  421.8846  
 ligand eigen vectors: 
|  -0.03435,    0.2262,   -0.9735|
|   -0.4586,    0.8619,    0.2164|
|     0.888,    0.4539,   0.07411|
INFO:: Protein centre at: xyz = (     41.53,     8.726,     12.87)
There are 1 clusers
Here are the top 10 clusers:
  Number: 0 # grid points: 264 score: 146.5952     
|   -0.1765,     0.981,  -0.08001|
|    0.2847,    0.1287,    0.9499|
|    0.9422,    0.1449,    -0.302|
(     55.49,     9.316,     20.62)   xyz = (      3.05,     1.281,    0.8881) eigenvalues: 131.0082 2545.3515 421.9402 
 found distance from reference centre 0.5679
PASS: test ligand from point
Entering test: test peak search non-close
reading mtz file...
Number of reflections: 17982
finding ASU unique map points...
Grid...Nuvw = ( 108, 132,  64)
doing fft...
done fft...
INFO:: peak filtering: npeaks: in: 5158 out: 2105
   There are 2105 peaks and 0 problem peaks
PASS: test peak search non-close
Entering test: test symop card
1 0 0
0 1 0
0 0 1
translations: -1.0000 0.0000 0.0000
PASS: test symop card
Entering test: test rotate round vector
INFO:: Reading coordinate file: /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb
 PDB file /lmb/home/pemsley/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
   0  O6  0.9397 -> 20.0000 degrees
   1  C6  0.9397 -> 20.0000 degrees
   2  C5  0.9397 -> 20.0000 degrees
   3  C4  0.9397 -> 20.0000 degrees
   4  N3  0.9397 -> 20.0000 degrees
   5  C2  0.9397 -> 20.0000 degrees
   6  N2  0.9397 -> 20.0000 degrees
   7 HN22 0.9397 -> 20.0000 degrees
   8 HN21 0.9397 -> 20.0000 degrees
   9  N1  0.9397 -> 20.0000 degrees
   10  HN1 0.9397 -> 20.0000 degrees
   11  N7  0.9397 -> 20.0000 degrees
   12  C8  0.9397 -> 20.0000 degrees
   13  H8  0.9397 -> 20.0000 degrees
   16  H1* 0.9397 -> 20.0000 degrees
   17  O4* 0.9397 -> 20.0000 degrees
   18  C4* 0.9397 -> 20.0000 degrees
   19  H4* 0.9397 -> 20.0000 degrees
   20  C5* 0.9397 -> 20.0000 degrees
   21 H5*1 0.9397 -> 20.0000 degrees
   22 H5*2 0.9397 -> 20.0000 degrees
   23  O5* 0.9397 -> 20.0000 degrees
   24 HO5* 0.9397 -> 20.0000 degrees
   25  C2* 0.9397 -> 20.0000 degrees
   26  H2* 0.9397 -> 20.0000 degrees
   27  O2* 0.9397 -> 20.0000 degrees
   28 HO2* 0.9397 -> 20.0000 degrees
   29  C3* 0.9397 -> 20.0000 degrees
   30  H3* 0.9397 -> 20.0000 degrees
   31  O3* 0.9397 -> 20.0000 degrees
   32  P   0.9397 -> 20.0000 degrees
   33  O1P 0.9397 -> 20.0000 degrees
   34  O3P 0.9397 -> 20.0000 degrees
   35  O2P 0.9397 -> 20.0000 degrees
PASS: test rotate round vector
Entering test: SSM sequence alignment output

--
 Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG
 Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG

 Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC

--
 Moving: D
 Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG

--
 Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG
 Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG

--
PASS: SSM sequence alignment output
ok

----------------------------------------------------------------------
Ran 123 tests in 83.816s

OK


test00_0 (__main__.PdbMtzTestFunctions)
Post Go To Atom no molecule ... ok
test01_0 (__main__.PdbMtzTestFunctions)
Close bad molecule ... ok
test02_0 (__main__.PdbMtzTestFunctions)
Read coordinates test ... ok
test03_0 (__main__.PdbMtzTestFunctions)
New molecule from bogus molecule ... ok
test03_1 (__main__.PdbMtzTestFunctions)
Don't crash on empty NCS from mmCIF file ... ok
test04_0 (__main__.PdbMtzTestFunctions)
New molecule from bogus atom selection ... ok
test05_0 (__main__.PdbMtzTestFunctions)
ins code change and Goto atom over an ins code break ... ok
test06_0 (__main__.PdbMtzTestFunctions)
Read a bogus map ... ok
test07_0 (__main__.PdbMtzTestFunctions)
Read MTZ test ... ok
test07_1 (__main__.PdbMtzTestFunctions)
Auto-read bad MTZ test ... ok
test08_0 (__main__.PdbMtzTestFunctions)
Map Sigma ... ok
test09_0 (__main__.PdbMtzTestFunctions)
Another Level Test ... ok
test09_1 (__main__.PdbMtzTestFunctions)
db-main makes mainchain ... ok
test10_0 (__main__.PdbMtzTestFunctions)
Set Atom Atribute Test ... ok
test11_0 (__main__.PdbMtzTestFunctions)
Add Terminal Residue Test ... ok
test11_1 (__main__.PdbMtzTestFunctions)
Adding residue by phi psi, no crash ... ok
test12_0 (__main__.PdbMtzTestFunctions)
Select by Sphere ... ok
test13_0 (__main__.PdbMtzTestFunctions)
Test Views ... ok
test13_1 (__main__.PdbMtzTestFunctions)
Delete Residue ... ok
test14_0 (__main__.PdbMtzTestFunctions)
Label Atoms and Delete ... ok
test15_0 (__main__.PdbMtzTestFunctions)
Rotamer outliers ... ok
test16_0 (__main__.PdbMtzTestFunctions)
Alt Conf Occ Sum Reset ... ok
test16_1 (__main__.PdbMtzTestFunctions)
Correct occupancies after auto-fit rotamer on alt-confed residue ... ok
test16_2 (__main__.PdbMtzTestFunctions)
Rotamers work on MSE ... ok
test16_3 (__main__.PdbMtzTestFunctions)
Hs are correctly swapped on a TYR ... ok
test16_4 (__main__.PdbMtzTestFunctions)
Splitting residue leaves no atoms with negative occupancy ... ok
test17_0 (__main__.PdbMtzTestFunctions)
Pepflip flips the correct alt confed atoms ... ok
test18_0 (__main__.PdbMtzTestFunctions)
Correction of CISPEP test ... ok
test19_0 (__main__.PdbMtzTestFunctions)
Refine Zone with Alt conf ... ok
test20_0 (__main__.PdbMtzTestFunctions)
Sphere Refine ... ok
test20_1 (__main__.PdbMtzTestFunctions)
Refinement gives useful results ... ok
test21_0 (__main__.PdbMtzTestFunctions)
Rigid Body Refine Alt Conf Waters ... ok
test22_0 (__main__.PdbMtzTestFunctions)
Setting multiple atom attributes ... ok
test23_0 (__main__.PdbMtzTestFunctions)
Tweak Alt Confs on Active Residue ... ok
test24_0 (__main__.PdbMtzTestFunctions)
Backrub rotamer ... ok
test25_0 (__main__.PdbMtzTestFunctions)
Libcif horne ... ok
test26_0 (__main__.PdbMtzTestFunctions)
Refmac Parameters Storage ... ok
test26_1 (__main__.PdbMtzTestFunctions)
OXT is added before TER record - add only one ... ok
test27_0 (__main__.PdbMtzTestFunctions)
The position of the oxygen after a mutation ... ok
test27_1 (__main__.PdbMtzTestFunctions)
TER is at the end of a nucleotide after mutation ... ok
test27_2 (__main__.PdbMtzTestFunctions)
C7 is removed on mutation from a DC ... ok
test27_3 (__main__.PdbMtzTestFunctions)
C7 is added on mutation to a DC ... ok
test28_0 (__main__.PdbMtzTestFunctions)
Deleting (non-existing) Alt conf and Go To Atom [JED] ... ok
test29_0 (__main__.PdbMtzTestFunctions)
Mask and difference map ... ok
test29_1 (__main__.PdbMtzTestFunctions)
Skeletonize a map ... ok
test29_2 (__main__.PdbMtzTestFunctions)
Simple Averaged maps ... ok
test30_0 (__main__.PdbMtzTestFunctions)
Make a glycosidic linkage ... ok
test30_1 (__main__.PdbMtzTestFunctions)
Refine an NAG-ASN Link ... ok
test31_0 (__main__.PdbMtzTestFunctions)
Test for flying hydrogens on undo ... ok
test32_0 (__main__.PdbMtzTestFunctions)
Test for mangling of hydrogen names from a PDB v 3.0 ... ok
test32_1 (__main__.PdbMtzTestFunctions)
Correct matching dictionary names from test name ... ok
test33_0 (__main__.PdbMtzTestFunctions)
Update monomer restraints ... ok
test33_1 (__main__.PdbMtzTestFunctions)
Write mmCIF restraints correctly ... ok
test34_0 (__main__.PdbMtzTestFunctions)
Refinement OK with zero bond esd ... ok
test35_0 (__main__.PdbMtzTestFunctions)
Change Chain IDs and Chain Sorting ... ok
test36_0 (__main__.PdbMtzTestFunctions)
Replace Fragment ... ok
test37_0 (__main__.PdbMtzTestFunctions)
Residues in Region of Residue ... ok
test38_0 (__main__.PdbMtzTestFunctions)
Residues in region of a point ... ok
test39_0 (__main__.PdbMtzTestFunctions)
Empty molecule on type selection ... ok
test40_0 (__main__.PdbMtzTestFunctions)
Set Rotamer ... ok
test41_0 (__main__.PdbMtzTestFunctions)
Rotamer names and scores are correct ... ok
test42_0 (__main__.PdbMtzTestFunctions)
Align and mutate a model with deletions ... ok
test42_1 (__main__.PdbMtzTestFunctions)
Renumber residues should be in seqnum order ... ok
test43_0 (__main__.PdbMtzTestFunctions)
Autofit Rotamer on Residue with Insertion codes ... ok
test44_0 (__main__.PdbMtzTestFunctions)
RNA base has correct residue type after mutation ... ok
test45_0 (__main__.PdbMtzTestFunctions)
DNA bases are the correct residue type after mutation ... ok
test46_0 (__main__.PdbMtzTestFunctions)
SegIDs are correct after mutate ... ok
test47_0 (__main__.PdbMtzTestFunctions)
TER on water chain is removed on adding a water by hand ... ok
test48_0 (__main__.PdbMtzTestFunctions)
TER on water chain is removed on adding waters automatically ... ok
test48_1 (__main__.PdbMtzTestFunctions)
Adding atoms to Many-Chained Molecule ... ok
test49_0 (__main__.PdbMtzTestFunctions)
Arrange waters round protein ... ok
test50_0 (__main__.PdbMtzTestFunctions)
Correct Segid After Add Terminal Residue ... ok
test51_0 (__main__.PdbMtzTestFunctions)
Correct Segid after NCS residue range copy ... ok
test52_0 (__main__.PdbMtzTestFunctions)
Merge Water Chains ... ok
test52_1 (__main__.PdbMtzTestFunctions)
Consolidated merge ... ok
test53_0 (__main__.PdbMtzTestFunctions)
LSQ by atom ... ok
test53_1 (__main__.PdbMtzTestFunctions)
LSQing changes the space-group and cell to that of the reference molecule ... ok
test53_2 (__main__.PdbMtzTestFunctions)
set_residue_name sets the correct residue ... ok
test53_3 (__main__.PdbMtzTestFunctions)
fit_protein_make_specs makes all specs ... ok
test54_0 (__main__.PdbMtzTestFunctions)
Phosphate distance in pucker analysis is sane ... ok
test60_0 (__main__.PdbMtzTestFunctions)
post_manipulation_hook_py test (replaces Hundreds of Ramachandran refinements) ... ok
test61_0 (__main__.PdbMtzTestFunctions)
Read/write gz coordinate files ... ok
test999_0 (__main__.PdbMtzTestFunctions)
Renumber residue range without overwriting coordinates. ... ok
test01_0 (__main__.ShelxTestFunctions)
Read small molecule .res file ... ok
test02_0 (__main__.ShelxTestFunctions)
Read hollander small molecule .res file ... ok
test03_0 (__main__.ShelxTestFunctions)
read shelx insulin with fcf ... ok
test04_0 (__main__.ShelxTestFunctions)
Write an INS from PDB test ... ok
test05_0 (__main__.ShelxTestFunctions)
new molecule by atom selection inherits shelx molecule flag ... ok
test06_0 (__main__.ShelxTestFunctions)
Addition of Terminal Residue on SHELX molecule has correct occupancy ... ok
test07_0 (__main__.ShelxTestFunctions)
Add water to SHELX molecule ... ok
test08_0 (__main__.ShelxTestFunctions)
Find Waters for a SHELXL molecule ... ok
test09_0 (__main__.ShelxTestFunctions)
NPD Anisotropic Atom [Mitch Miller] ... ok
test10_0 (__main__.ShelxTestFunctions)
close shelx molecules ... ok
test11_0 (__main__.ShelxTestFunctions)
Aniso Bs in P21 ... ok
test12_0 (__main__.ShelxTestFunctions)
Don't crash on reading a strange HAT file ... ok
test01_0 (__main__.LigandTestFunctions)
Get monomer test ... ok
test02_0 (__main__.LigandTestFunctions)
Set Bond thickness test ... ok
test03_0 (__main__.LigandTestFunctions)
Delete all-molecule Hydrogens ... ok
test04_0 (__main__.LigandTestFunctions)
Non-Autoloads ... ok
test05_0 (__main__.LigandTestFunctions)
Move and Refine Ligand test ... ok
test06_0 (__main__.LigandTestFunctions)
Many Molecules - Ligand Fitting ... ok
test07_0 (__main__.LigandTestFunctions)
Flip residue (around eigen vectors) ... ok
test08_0 (__main__.LigandTestFunctions)
Test dipole ... ok
test09_0 (__main__.LigandTestFunctions)
Reading new dictionary restraints replaces ... ok
test10_0 (__main__.LigandTestFunctions)
Pyrogen Runs OK? ... ok
test01_0 (__main__.CootaneerTestFunctions)
Assignment of new PIR sequence overwrites old assignment ... ok
test02_0 (__main__.CootaneerTestFunctions)
Cootaneer Beta Strand ... ok
test01_0 (__main__.RnaGhostsTestFunctions)
RNA NCS Ghosts ... ok
test01_0 (__main__.SsmTestFunctions)
SSM - Frank von Delft's Example ... ok
test02_0 (__main__.SsmTestFunctions)
SSM - Alice Dawson's Example ... ok
test03_0 (__main__.SsmTestFunctions)
SSM by atom selection [JED Example] ... ok
test01_1 (__main__.NcsTestFunctions)
NCS maps test ... ok
test02_0 (__main__.NcsTestFunctions)
NCS chains info ... ok
test03_0 (__main__.NcsTestFunctions)
NCS deviation info ... ok
test04_0 (__main__.NcsTestFunctions)
NCS Residue Range copy ... ok
test05_0 (__main__.NcsTestFunctions)
NCS Residue Range edit to all chains ... ok
test06_0 (__main__.NcsTestFunctions)
Manual NCS ghosts generates correct NCS chain ids ... ok
test07_0 (__main__.NcsTestFunctions)
NCS maps overwrite existing maps ... ok
test01_0 (__main__.UtilTestFunctions)
Test key symbols ... ok
test02_0 (__main__.UtilTestFunctions)
Test running a scheme function ... ok
test03_0 (__main__.UtilTestFunctions)
Internal/External Molecule Numbers match ... ok
test05_0 (__main__.UtilTestFunctions)
Import gobject ... ok
test_00 (__main__.InternalTestFunctions)
Test internal functions ... ok

----------------------------------------------------------------------
Ran 123 tests in 83.816s

OK


Unitest skip does not exist!
The following tests were skipped and marked as passed:
    Libcif horne


INFO:: Command: (close-molecule 0)
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gc: collectable <cell 0x2aec66941b78>
gc: collectable <cell 0x2aec663f9c58>
gc: collectable <cell 0x2aec66952910>
gc: collectable <function 0x2aec673af758>
gc: collectable <tuple 0x2aec6695ff00>
gc: collectable <function 0x2aec673af6e0>

FINALLY collect some GARBAGE

BL INFO:: no of collected carbage items 6

BL DEBUG:: list of garbage items:

     <cell at 0x2aec66941b78: function object at 0x2aec673af6e0>
     <cell at 0x2aec663f9c58: function object at 0x2aec673af758>
     <cell at 0x2aec66952910: module object at 0x2aec638d8868>
     <function skip_to_chain_internal at 0x2aec673af758>
     (<cell at 0x2aec66941b78: function object at 0x2aec673af6e0>, <cell at 0x2aec663f9c58: function object at 0x2aec673af758>, <cell at 0x2aec66952910: module object at 0x2aec638d8868>)
     <function skip_to_chain at 0x2aec673af6e0>

Detailed information for functions:

  BL INFO:: garbage item and location:
    <function skip_to_chain_internal at 0x2aec673af758>
    <code object skip_to_chain_internal at 0x2aec63cfce30, file "/lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/lib/python2.7/site-packages/coot/ncs.py", line 39>

  BL INFO:: garbage item and location:
    <function skip_to_chain at 0x2aec673af6e0>
    <code object skip_to_chain at 0x2aec63cfceb0, file "/lmb/home/pemsley/autobuild/Linux-pcterm37.lmb.internal-pre-release-gtk2-python/lib/python2.7/site-packages/coot/ncs.py", line 56>

INFO:: Command: (use-graphics-interface-state)
INFO:: Command: (stereo-mode-state)
INFO:: Command: (stereo-mode-state)
INFO:: Command: (save-state)
Good morning Paul Emsley PI Garib Murshudov added 28092012. Welcome to Coot 0.8.8-pre.
ObjectCache: Leaked 0003 refs to <C 2c 2 Nuvw = ( 160, 160, 336)>
ObjectCache: Leaked 0003 refs to <C 2c 2>
test_coot_python: coot test passed