testing with python unittest
testing with python unittest
currently we are here:
/lmb/home/pemsley/autobuild/building/lg19.lmb.internal_2017-08-01__T23_30_02/coot-0.8.9-pre
/lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-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-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/standard-residues.pdb
 PDB file /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-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-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Paul, Welcome to Coot version 0.8.9-pre
(set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.8.9-pre")
(use-graphics-interface-state)
Running python script /lmb/home/pemsley/.coot-preferences/contact_dots.py
name 'coot_menubar_menu' is not defined
Running python script /lmb/home/pemsley/.coot-preferences/coot_probe_dots.py
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 0.8.9-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/chain-refine.scm
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 22.00)
(set-swap-difference-map-colours 0)
(set-colour-map-rotation-for-map 14.00)
(set-active-map-drag-flag 1)
(set-idle-function-rotate-angle  1.00)
load /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/kill-side-chain.scm
load /lmb/home/pemsley/.coot-preferences/morph-march.scm
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
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
WARNING:: 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_Wed_Aug__2_00:49:36_2017_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_Wed_Aug__2_00:49:36_2017_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_Wed_Aug__2_00:49:36_2017_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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.075 seconds to read MTZ file
INFO:: 0.051 seconds to initialize map
INFO:: 0.041 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.014 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.299 seconds for contour map
INFO:: 0.48 seconds in total
ok
test07_1 (__main__.PdbMtzTestFunctions)
Auto-read bad MTZ test ... WARNING:: file xx-missing.mtz does not exist
   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 <<<<<<
CCP4MTZfile: open_read - File missing or corrupted: /lmb/home/pemsley/data/greg-data/broken.mtz
INFO:: not an mtz file: /lmb/home/pemsley/data/greg-data/broken.mtz
   got status:  ()
ok
test08_0 (__main__.PdbMtzTestFunctions)
Map Sigma ...    INFO:: map sigmas 0.311500996351 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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.028 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.011 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.239 seconds for contour map
INFO:: 0.305 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
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-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures successfully opened
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
29 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1et1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2b.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
24 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g2y.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
72 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jk3.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
145 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jl1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
226 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fsg.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
228 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1k7c.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
9 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1euw.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
174 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i4u.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i8o.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
45 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i12.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
218 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g61.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
56 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f94.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i27.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ejg.pdb
There was an error reading /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-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-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
129 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e29.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
171 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g66.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c75.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
543 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hbn.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
33 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gmx.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
23 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g6x.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
349 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ka1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
35 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1koi.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
364 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ga6.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
13 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g4i.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
52 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e9g.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
155 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fye.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i40.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
108 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f86.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
172 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1eb6.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
20 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hg7.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
208 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jg1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
119 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1dy5.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
14 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1g7a.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
318 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ds1.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
294 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hvb.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
68 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jbe.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
131 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j9b.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
54 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i2t.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jfb.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
136 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1ird.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
247 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jcl.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
75 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1iqz.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
494 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1e4m.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
64 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0v.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
137 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdo.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1gk9.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
520 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hdh.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
326 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1i0d.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
4 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1fn8.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
411 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1hyo.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
51 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1kth.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
149 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1j98.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
205 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1es9.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
140 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f4p.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
143 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1f9v.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
0 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1heu.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
106 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h4x.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
123 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1jf8.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
142 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1h97.pdb
Adding fragments from: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
127 fragments garnered from /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/reference-structures/1c7k.pdb
INFO:: 8375 fragments found in total       of which 0 were 5 peptides 
target fragment start res: 10 had 29 db fragment hits, ilength=6
target fragment start res: 13 had 1772 db fragment hits, ilength=6
breaking out of match_target_fragment 6 with iresno= 16
merge fragments 10 to 20 with 2 fit sets to merge
The merging is complete
mainchain_fragment from 10 to 20
done mainchain_fragment
successfully set cell and symmetry
INFO:: 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
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
WARNING:: 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_Wed_Aug__2_00:49:40_2017_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
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 
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_Wed_Aug__2_00:49:40_2017_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
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 ... 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: (seqnum-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: (seqnum-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: (seqnum-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: (seqnum-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
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_Wed_Aug__2_00:49:42_2017_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 ... 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_Wed_Aug__2_00:49:42_2017_modification_0.pdb.gz
INFO:: Command: (delete-residue 12 "B" 10 "")
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:49:42_2017_modification_1.pdb.gz
INFO:: Command: (delete-residue 12 "B" 11 "")
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:49:42_2017_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
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
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 141) at 9.94491
    Final Estimated RMS Z Scores:
bonds:      0.0954112
angles:     0.665415
torsions:   N/A 
planes:     0.648876
non-bonded: 0
chiral vol: 0.590025
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 8.033
debug:: restraints results 1 5 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_res098.pdb_Wed_Aug__2_00:49:44_2017_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
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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.027 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.011 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.269 seconds for contour map
INFO:: 0.334 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_Wed_Aug__2_00:49:45_2017_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_Wed_Aug__2_00:49:45_2017_modification_1.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 12.0528
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
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_Wed_Aug__2_00:49:46_2017_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
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_Wed_Aug__2_00:49:46_2017_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
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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.03 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.032 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.013 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.328 seconds for contour map
INFO:: 0.404 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_Wed_Aug__2_00:49:48_2017_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
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_Wed_Aug__2_00:49:49_2017_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
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 0x3946880
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_Wed_Aug__2_00:49:51_2017_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_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_Wed_Aug__2_00:49:51_2017_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: 4091.97
    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 118) at -4925.75
    Final Estimated RMS Z Scores:
bonds:      0.933786
angles:     0.807678
torsions:   N/A 
planes:     2.58973
non-bonded: 0.181009
chiral vol: 0.374877
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 14.972
Refinement elapsed time: 0.015
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_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_Wed_Aug__2_00:49:51_2017_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_Wed_Aug__2_00:49:51_2017_modification_5.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 8.73281
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: -6099.8
    Initial RMS Z values
bonds:      0.904877
angles:     1.49461
torsions:   N/A 
planes:     3.14541
non-bonded: 0.482928
chiral vol: 0.446824
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 82) at -6206.77
    Final Estimated RMS Z Scores:
bonds:      0.910903
angles:     0.733065
torsions:   N/A 
planes:     2.6599
non-bonded: 0.0848076
chiral vol: 0.208863
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 15.112
Refinement elapsed time: 0.012
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_Aug__2_00:49:51_2017_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
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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.031 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.031 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.013 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.321 seconds for contour map
INFO:: 0.397 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: -2794.63
    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 72) at -2931.62
    Final Estimated RMS Z Scores:
bonds:      1.12653
angles:     1.40458
torsions:   N/A 
planes:     0.421965
non-bonded: 3.29028
chiral vol: 0.792588
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 16.504
Refinement elapsed time: 0.007
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:49:52_2017_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
   refined moved: d= 0.295132018165
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
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_Wed_Aug__2_00:49:54_2017_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
   0 trans-peptide links
   0 parallel plane restraints
Flanking residue restraints: 
   5 bond    links
   15 angle   links
   10 plane   links
   0 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 1979 non-bonded restraints
initial distortion_score: -21111
    Initial RMS Z values
bonds:      1.74258
angles:     1.26763
torsions:   N/A 
planes:     0.838264
non-bonded: 0.000533565
chiral vol: 0.894378
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 73) at -21507.2
    Final Estimated RMS Z Scores:
bonds:      1.14532
angles:     0.684659
torsions:   N/A 
planes:     0.544685
non-bonded: 1.50627e-05
chiral vol: 0.208775
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 18.936
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Aug__2_00:49:54_2017_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
   0 trans-peptide links
   0 parallel plane restraints
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
   0 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 1393 non-bonded restraints
initial distortion_score: -7984.72
    Initial RMS Z values
bonds:      0.980695
angles:     1.01754
torsions:   N/A 
planes:     1.78749
non-bonded: 4.74047
chiral vol: 10.2816
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 125) at -15999.1
    Final Estimated RMS Z Scores:
bonds:      1.95686
angles:     1.73857
torsions:   N/A 
planes:     1.66012
non-bonded: 0.0447882
chiral vol: 2.09649
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 20.383
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_Aug__2_00:49:54_2017_modification_2.pdb.gz
INFO:: replace_coords: 41 atoms updated.
======= got bond length 1.28808209252
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
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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.026 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.011 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.278 seconds for contour map
INFO:: 0.342 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: -6107.02
    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 14) at -11756.1
    Final Estimated RMS Z Scores:
bonds:      1.8405
angles:     1.7681
torsions:   N/A 
planes:     2.01149
non-bonded: 0.0826445
chiral vol: 1.99953
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 22.032
Refinement elapsed time: 0.042
   refinement results: ['', 0, [['Bonds', 'Bonds:    1.840', 1.8404970169067383], ['Angles', 'Angles:   1.768', 1.7681007385253906], ['Planes', 'Planes:   2.011', 2.0114858150482178], ['Non-bonded', 'Non-bonded:   0.287', 0.28747954964637756], ['Chirals', 'Chirals:   2.000', 1.9995266199111938]]]
::::   ow factor 1.9049025476
   INFO:: setting refinement weight to 16.5350580955 from 60.0 / ( 1.9049025476 * 1.9049025476 )
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: 1793.68
    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 140) at -3158.93
    Final Estimated RMS Z Scores:
bonds:      0.697622
angles:     0.866569
torsions:   N/A 
planes:     1.68709
non-bonded: 0.00606403
chiral vol: 0.806408
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 22.09
Refinement elapsed time: 0.057
   refinement results: ['', 0, [['Bonds', 'Bonds:    0.698', 0.6976221203804016], ['Angles', 'Angles:   0.867', 0.8665685057640076], ['Planes', 'Planes:   1.687', 1.6870890855789185], ['Non-bonded', 'Non-bonded:   0.078', 0.0778719112277031], ['Chirals', 'Chirals:   0.806', 0.8064076900482178]]]
::::   ow factor 1.01442185044
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
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_Wed_Aug__2_00:49:59_2017_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
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 
INFO:: Command: (copy-molecule 29)
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Wed_Aug__2_00:50:00_2017_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_backrub-fragment.pdb_Wed_Aug__2_00:50:00_2017_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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.036 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.033 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.013 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.264 seconds for contour map
INFO:: 0.347 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
WARNING:: 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_Wed_Aug__2_00:50:02_2017_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
WARNING:: 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_Wed_Aug__2_00:50:04_2017_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
WARNING:: 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_Wed_Aug__2_00:50:05_2017_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
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_Wed_Aug__2_00:50:07_2017_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
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_Wed_Aug__2_00:50:08_2017_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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.028 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.027 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.011 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.25 seconds for contour map
INFO:: 0.317 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:: 0.027 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.026 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.012 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.255 seconds for contour map
INFO:: 0.32 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
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
INFO:: Map statistics: mean: -0.00140896 st.d: 0.305562
INFO:: Map statistics:  min: -0.921659   max: 3.05176
Map statistics: mean: -0.00140896 st.d: 0.305562
Map statistics: min: -0.921659, max: 3.05176
 -0.871991    10
 -0.772655    72
  -0.67332    614
 -0.573984    3970
 -0.474649    16922
 -0.375313    47064
 -0.275978    80118
 -0.176642    105928
-0.0773069    131011
 0.0220286    142638
  0.121364    80192
    0.2207    37039
  0.320035    20148
  0.419371    14894
  0.518706    11885
  0.618042    10488
  0.717377    8813
  0.816713    7252
  0.916048    5646
   1.01538    4143
   1.11472    2992
   1.21405    2070
   1.31339    1406
   1.41273    857
   1.51206    523
    1.6114    288
   1.71073    155
   1.81007    64
    1.9094    36
   2.00874    17
   2.10807    8
   2.20741    2
   2.30675    5
   2.40608    4
   2.50542    2
   2.60475    1
   2.70409    1
   2.80342    1
   2.90276    0
   3.00209    1
   3.10143    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: [0.8227399587631226, 1.0119965076446533, 1.0171315670013428, 1.068248987197876, 0.7381036281585693, 0.801753580570221, 0.6875786781311035, 0.6362037658691406, 1.0157028436660767, 0.9525023698806763, 0.9898293018341064]  low values: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
INFO:: Map statistics: mean: -0.00140896 st.d: 0.0605043
INFO:: Map statistics:  min: -2.99276   max: 0.774316
Map statistics: mean: -0.00140896 st.d: 0.0605043
Map statistics: min: -2.99276, max: 0.774316
  -2.94567    2
  -2.85149    2
  -2.75732    1
  -2.66314    2
  -2.56896    3
  -2.47479    3
  -2.38061    1
  -2.28643    4
  -2.19226    4
  -2.09808    3
   -2.0039    4
  -1.90973    4
  -1.81555    6
  -1.72137    12
  -1.62719    20
  -1.53302    21
  -1.43884    29
  -1.34466    47
  -1.25049    87
  -1.15631    85
  -1.06213    153
 -0.967957    182
  -0.87378    266
 -0.779603    331
 -0.685426    378
 -0.591249    415
 -0.497072    517
 -0.402895    588
 -0.308718    704
 -0.214541    858
 -0.120364    1154
-0.0261874    723063
 0.0679895    2120
  0.162166    2190
  0.256343    1772
   0.35052    1353
  0.444697    623
  0.538874    215
  0.633051    49
  0.727228    9
  0.821405    0
   diff-high-values: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]  diff-low-values: [-0.5536488890647888, -0.9707267880439758, -0.6932032108306885, -0.848896324634552, -0.8271133899688721, -1.0860068798065186, -1.2907466888427734, -1.1838661432266235, -0.947303831577301, -0.893179178237915]
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
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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.027 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.011 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.273 seconds for contour map
INFO:: 0.337 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 2.2
INFO grid sampling...Nuvw = ( 160, 192,  96)
INFO:: 0.026 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.027 seconds for FFT
INFO:: Map statistics: mean: 1.22049e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.921659   max: 3.05176
INFO:: 0.011 seconds for statistics
      Map mean: ........ 1.22049e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.275 seconds for contour map
INFO:: 0.34 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:: 0.027 seconds to read MTZ file
INFO:: 0.039 seconds to initialize map
INFO:: 0.036 seconds for FFT
INFO:: Map statistics: mean: 1.13088e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.877519   max: 3.07133
INFO:: 0.016 seconds for statistics
      Map mean: ........ 1.13088e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.07133
      Map minimum: ..... -0.877519
INFO:: 0.391 seconds for contour map
INFO:: 0.509 seconds in total
INFO:: multiplying map (function index) 0 Nuvw = ( 160, 192,  96) by 1
INFO:: multiplying map (function index) 1 Nuvw = ( 180, 216, 108) by 1
INFO:: Map statistics: mean: -3.34696e-06 st.d: 0.311048
INFO:: Map statistics:  min: -0.916532   max: 3.05151
Map statistics: mean: -3.34696e-06 st.d: 0.311048
Map statistics: min: -0.916532, max: 3.05151
 -0.866931    10
  -0.76773    76
 -0.668529    693
 -0.569328    4378
 -0.470127    18338
 -0.370926    49769
 -0.271725    82935
 -0.172524    109167
-0.0733227    133898
 0.0258784    127242
  0.125079    79379
  0.224281    36898
  0.323482    20503
  0.422683    15332
  0.521884    12363
  0.621085    10886
  0.720286    9118
  0.819487    7521
  0.918688    5833
   1.01789    4256
   1.11709    3092
   1.21629    2109
   1.31549    1444
   1.41469    867
   1.51389    533
    1.6131    302
    1.7123    160
    1.8115    68
    1.9107    40
    2.0099    20
    2.1091    11
    2.2083    7
    2.3075    9
    2.4067    5
   2.50591    5
   2.60511    4
   2.70431    2
   2.80351    4
   2.90271    1
   3.00191    2
   3.10111    0
INFO:: Map statistics: mean: 3.34818e-06 st.d: 0.00108591
INFO:: Map statistics:  min: -0.0109202   max: 0.00950789
Map statistics: mean: 3.34818e-06 st.d: 0.00108591
Map statistics: min: -0.0109202, max: 0.00950789
-0.0106648    1
-0.0101541    4
-0.00964341    5
-0.00913271    7
-0.00862201    8
-0.00811131    17
-0.00760061    17
-0.00708991    20
-0.0065792    18
-0.0060685    43
-0.0055578    95
-0.0050471    231
-0.0045364    544
-0.0040257    1167
-0.00351499    2161
-0.00300429    4144
-0.00249359    8444
-0.00198289    16358
-0.00147219    32960
-0.000961487    73381
-0.000450785    158320
5.99161e-05    204515
0.000570618    125580
0.00108132    51959
0.00159202    23884
0.00210272    12694
0.00261342    7552
0.00312413    4844
0.00363483    3115
0.00414553    1977
0.00465623    1264
0.00516693    844
0.00567763    507
0.00618833    274
0.00669904    169
0.00720974    74
0.00772044    47
0.00823114    18
0.00874184    10
0.00925254    8
0.00976325    0
  INFO:: map sigmas: normal 0.311048001051 and diff-map: 0.00108590547461
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-3.pdb" 1)
WARNING:: Error reading /lmb/home/pemsley/data/greg-data/multi-carbo-coot-3.pdb
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
INFO:: NCS chain comparison 4/110
Molecule 48 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:: 0.027 seconds to read MTZ file
INFO:: 0.009 seconds to initialize map
INFO:: 0.013 seconds for FFT
INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.875045   max: 2.97757
INFO:: 0.004 seconds for statistics
      Map mean: ........ 1.05439e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.081 seconds for contour map
INFO:: 0.134 seconds in total
INFO:: dictionary does not already have NAG dynamic add it now
......... checking for /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab
..that failed - trying  /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/share/coot/NAG-decorations.tab
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_0.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_1.pdb.gz
INFO:: link torsion generated from link bond restraint
ERROR:: null link 0 in ref
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_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
   0 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 1039 non-bonded restraints
initial distortion_score: 30660.5
    Initial RMS Z values
bonds:      0.360748
angles:     0.606408
torsions:   N/A 
planes:     0.68341
non-bonded: 30.3363
chiral vol: 0.444926
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 82) at -905.506
    Final Estimated RMS Z Scores:
bonds:      2.3209
angles:     1.94418
torsions:   N/A 
planes:     1.13491
non-bonded: 0.0629911
chiral vol: 1.16184
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 45.197
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_modification_3.pdb.gz
INFO:: replace_coords: 22 atoms updated.
INFO:: link torsion generated from link bond restraint
ERROR:: null link 0 in ref
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_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
   0 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 894 non-bonded restraints
initial distortion_score: -159.726
    Initial RMS Z values
bonds:      2.3209
angles:     1.94418
torsions:   N/A 
planes:     1.13491
non-bonded: 0.982695
chiral vol: 1.16184
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 136) at -1073.99
    Final Estimated RMS Z Scores:
bonds:      2.27428
angles:     1.71843
torsions:   N/A 
planes:     0.816347
non-bonded: 0.0708186
chiral vol: 1.14152
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 45.866
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_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
   0 trans-peptide links
   0 parallel plane restraints
INFO:: make_restraints(): made 805 non-bonded restraints
initial distortion_score: 527.093
    Initial RMS Z values
bonds:      2.27428
angles:     1.71843
torsions:   N/A 
planes:     0.816347
non-bonded: 2.06757
chiral vol: 1.14152
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 48) at -945.462
    Final Estimated RMS Z Scores:
bonds:      2.30866
angles:     1.92882
torsions:   N/A 
planes:     1.13624
non-bonded: 0.0791371
chiral vol: 1.12258
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 45.968
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb2qc1-sans-cho.pdb_Wed_Aug__2_00:50:20_2017_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
Molecule 50 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 70) at 0.248183
    Final Estimated RMS Z Scores:
bonds:      0.0122184
angles:     0.0948581
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.145399
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 49.236
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: undo molecule number set to: 50
INFO:: Command: (set-undo-molecule 50)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_1.pdb.gz
restoring from backup 2 2
INFO:: Reading coordinate file: coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_0.pdb.gz
 PDB file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_modification_0.pdb.gz has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
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 70) at 0.248183
    Final Estimated RMS Z Scores:
bonds:      0.0122184
angles:     0.0948581
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.145399
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 49.293
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-VAL.pdb_Wed_Aug__2_00:50:25_2017_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
WARNING:: No Symmetry for this model
Molecule 51 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 165) at 0.474695
    Final Estimated RMS Z Scores:
bonds:      0.00942912
angles:     0.121017
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.138512
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 52.695
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Wed_Aug__2_00:50:28_2017_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
plane restraint: [plane-restraint: plan  {12 atoms} : CB  0.02: : CG  0.02: : CD1 0.02: : CE1 0.02: : CZ  0.02: : CE2 0.02: : CD2 0.02: : OH  0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ]
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: 2026.18
    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 62) at -1103.08
    Final Estimated RMS Z Scores:
bonds:      0.831304
angles:     0.595276
torsions:   N/A 
planes:     0.510595
non-bonded: 0.0856199
chiral vol: 0.26391
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 52.746
Refinement elapsed time: 0.015
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:50:29_2017_modification_0.pdb.gz
INFO:: replace_coords: 12 atoms updated.
  Bond-length:  2.6034531676
   pass intermediate 2.8 tolerance test
looping over restraint
plane restraint: [plane-restraint: plan  {12 atoms} : CB  0.02: : CG  0.02: : CD1 0.02: : CE1 0.02: : CZ  0.02: : CE2 0.02: : CD2 0.02: : OH  0.02: : HD1 0.02: : HE1 0.02: : HE2 0.02: : HD2 0.02: ]
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: 1354.88
    Initial RMS Z values
bonds:      14.3437
angles:     0.595276
torsions:   N/A 
planes:     0.510595
non-bonded: 0
chiral vol: 0.26391
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 52) at -1200.38
    Final Estimated RMS Z Scores:
bonds:      0.295138
angles:     0.273537
torsions:   N/A 
planes:     0.782205
non-bonded: 0
chiral vol: 0.152028
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 52.787
Refinement elapsed time: 0.022
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:50:29_2017_modification_1.pdb.gz
INFO:: replace_coords: 12 atoms updated.
  OK plane atom   CB 
  Bond-length:  1.51797614189
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
Molecule 53 read successfully
DEBUG:: there were 1 types with no dictionary 
::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_ACT.cif -999999 0
Welcome to Coot
looping over restraint
plane restraint: [plane-restraint: plan-1  {4 atoms} : C   0.02: : O   0.02: : OXT 0.02: : CH3 0.02: ]
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: 4848.68
    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 2) at -295.197
    Final Estimated RMS Z Scores:
bonds:      0.0561422
angles:     0.371911
torsions:   N/A 
planes:     0.0717946
non-bonded: 0
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 56.288
Refinement elapsed time: 0.017
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-ACT.pdb_Wed_Aug__2_00:50:32_2017_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
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 54 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_0.pdb.gz
istat: ; 1
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_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_Wed_Aug__2_00:50:37_2017_modification_2.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_3.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_4.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_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_Wed_Aug__2_00:50:37_2017_modification_6.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_7.pdb.gz
INFO:: Command: (n-chains 54)
INFO:: Command: (chain_id 54 0)
INFO:: Command: (chain_id 54 1)
INFO:: Command: (chain_id 54 2)
INFO:: Command: (chain_id 54 3)
INFO:: Command: (chain_id 54 4)
INFO:: Command: (chain_id 54 5)
INFO:: Command: (chain_id 54 6)
INFO:: Command: (chain_id 54 7)
INFO:: Command: (chain_id 54 8)
ok
test36_0 (__main__.PdbMtzTestFunctions)
Replace Fragment ... INFO:: Command: (copy-molecule 0)
INFO:: Command: (update-go-to-atom-window-on-new-mol)
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:37_2017_modification_0.pdb.gz
INFO:: replace_coords: 1465 atoms updated.
INFO:: Command: (replace-fragement 55 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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 57 read successfully
DEBUG:: there were 0 types with no dictionary 
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_Wed_Aug__2_00:50:41_2017_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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 58 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (turn-off-backup 58)
INFO:: Command: (rotamer-score 58 "A" 28 "")
   Rotamer 0 : m-85 100.0
INFO:: Command: (rotamer-score 58 "A" 28 "")
   Rotamer 1 : t80 90.1668395996
INFO:: Command: (rotamer-score 58 "A" 28 "")
   Rotamer 2 : p90 50.7077865601
INFO:: Command: (rotamer-score 58 "A" 28 "")
   Rotamer 3 : m -30  21.4231548309
INFO:: Command: (rotamer-score 58 "A" 28 "")
   Rotamer 4 : m -30  21.4231548309
INFO:: Command: (turn-on-backup 58)
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
INFO:: NCS chain comparison 50/87
Molecule 59 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: aligning to mol number 59 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_Wed_Aug__2_00:50:50_2017_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: 8 "A" 1 ""] -> ASP
      [spec: 8 "A" 2 ""] -> VAL
      [spec: 8 "A" 3 ""] -> SER
      [spec: 8 "A" 11 ""] -> LEU
      [spec: 8 "A" 12 ""] -> PRO
      [spec: 8 "A" 13 ""] -> PRO
      [spec: 444383608 "A" 62 ""] -> PRO
      [spec: 444383608 "A" 63 ""] -> GLY
   Deletions:
      [spec: 444383608 "A" 24 ""]
      [spec: 444383608 "A" 33 ""]
   Mutations:
apply resno updates... 
Applied 3 insertions 
Applied 0 mutations 
Applied 2 deletions 
INFO:: Command: (write-pdb-file 59 "mutated.pdb")
    ::::: [59, 'A', 1, ''] False False
    ::::: [59, 'A', 4, ''] True True
    ::::: [59, 'A', 59, ''] True True
    ::::: [59, 'A', 60, ''] False False
    ::::: [59, 'A', 61, ''] False False
    ::::: [59, 'A', 93, ''] True True
    ::::: [59, '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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 60 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:50:53_2017_modification_0.pdb.gz
INFO:: Command: (renumber-residue-range 60 "A" 10 20 100)
INFO:: Command: (seqnum-from-serial-number 60 "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
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_Wed_Aug__2_00:50:57_2017_modification_0.pdb.gz
INFO:: Command: (renumber-residue-range 61 "A" 10 20 -100)
INFO:: Command: (seqnum-from-serial-number 61 "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
WARNING:: No Symmetry for this model
INFO:: NCS chain comparison 15/212
INFO:: NCS chain comparison 7/212
INFO:: NCS chain comparison 10/215
Molecule 62 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:: 0.024 seconds to read MTZ file
INFO:: 0.005 seconds to initialize map
INFO:: 0.01 seconds for FFT
INFO:: Map statistics: mean: 8.66951e-11 st.d: 0.260405
INFO:: Map statistics:  min: -1.03389   max: 1.71787
INFO:: 0.005 seconds for statistics
      Map mean: ........ 8.66951e-11
      Map sigma: ....... 0.260405
      Map maximum: ..... 1.71787
      Map minimum: ..... -1.03389
INFO:: 0.028 seconds for contour map
INFO:: 0.072 seconds in total
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Wed_Aug__2_00:51:01_2017_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" 62 63 0  0.00)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb3hfl.ent_Wed_Aug__2_00:51:01_2017_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
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")
INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_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 64 "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
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")
INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:51:01_2017_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 "" "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
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG")
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 66 "A" 2 "" "DC")
  mutated base to type DC
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 66 "A" 2 "" "DG")
  mutated base to type DG
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 66 "A" 2 "" "DA")
  mutated base to type DA
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 66 "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
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG")
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 "" "Cd")
  mutated base to type Cd
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 "" "Gd")
  mutated base to type Gd
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 "" "Ad")
  mutated base to type Ad
INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_Aug__2_00:51:01_2017_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 "" "Td")
  mutated base to type Td
ok
test46_0 (__main__.PdbMtzTestFunctions)
SegIDs are correct after mutate ... 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_Wed_Aug__2_00:51:01_2017_modification_0.pdb.gz
INFO:: Command: (mutate 68 "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
WARNING:: No Symmetry for this model
Molecule 69 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_Wed_Aug__2_00:51:05_2017_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 69 "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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 70 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: 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 -0.0338214 stdev: 0.146177)
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 = (     28.11,     32.19,     9.322) is too big to be water
INFO:: cluster at xyz = (     70.02,     19.14,     18.63) is too big to be water
INFO:: cluster at xyz = (     52.69,      10.8,     11.54) is too big to be water
INFO:: cluster at xyz = (      73.3,     12.31,     14.45) is too big to be water
INFO:: cluster at xyz = (     39.77,     8.163,     19.52) is too big to be water
INFO:: cluster at xyz = (      53.3,    -4.948,    -2.745) is too big to be water
INFO:: cluster at xyz = (     40.96,     7.032,     16.25) is too big to be water
INFO:: found 55 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_Wed_Aug__2_00:51:09_2017_modification_0.pdb.gz
INFO:: Adding to solvent chain: D
INFO:: Command: (write-pdb-file 70 "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
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:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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_Wed_Aug__2_00:51:14_2017_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
WARNING:: No Symmetry for this model
Molecule 72 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_Wed_Aug__2_00:51:21_2017_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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 73 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pathological-water-test.pdb_Wed_Aug__2_00:51:25_2017_modification_0.pdb.gz
INFO:: moved 181 water molecules
INFO:: Command: (write-pdb-file 73 "waters-moved-failure.pdb")
ok
test50_0 (__main__.PdbMtzTestFunctions)
Correct Segid After Add Terminal Residue ... 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:: 0.058 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.024 seconds for FFT
INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.875045   max: 2.97757
INFO:: 0.006 seconds for statistics
      Map mean: ........ 1.05439e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.103 seconds for contour map
INFO:: 0.191 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
WARNING:: 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_Wed_Aug__2_00:51:25_2017_modification_0.pdb.gz
INFO:: Command: (add-terminal-residue 74 "A" 93 1)
ok
test51_0 (__main__.PdbMtzTestFunctions)
Correct Segid after NCS residue range copy ... INFO:: Command: (copy-molecule 0)
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 76 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 76 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_Wed_Aug__2_00:51:26_2017_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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 77 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (turn-off-backup 77)
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 77 "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 77 "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 77 "F" 16 20 2)
INFO:: Command: (n-chains 77)
INFO:: Command: (chain_id 77 0)
INFO:: Command: (chain_id 77 1)
INFO:: Command: (chain_id 77 2)
INFO:: Command: (chain_id 77 3)
INFO:: Command: (chain_id 77 4)
INFO:: Command: (is-solvent-chain-p 77 "A")
INFO:: Command: (is-solvent-chain-p 77 "B")
INFO:: Command: (is-solvent-chain-p 77 "D")
INFO:: Command: (is-solvent-chain-p 77 "E")
INFO:: Command: (is-solvent-chain-p 77 "F")
INFO:: Command: (resname-from-serial-number 77 "D" 0)
INFO:: Command: (seqnum-from-serial-number 77 "D" 0)
INFO:: Command: (insertion-code-from-serial-number 77 "D" 0)
INFO:: Command: (resname-from-serial-number 77 "D" 1)
INFO:: Command: (seqnum-from-serial-number 77 "D" 1)
INFO:: Command: (insertion-code-from-serial-number 77 "D" 1)
INFO:: Command: (resname-from-serial-number 77 "D" 2)
INFO:: Command: (seqnum-from-serial-number 77 "D" 2)
INFO:: Command: (insertion-code-from-serial-number 77 "D" 2)
INFO:: Command: (resname-from-serial-number 77 "D" 3)
INFO:: Command: (seqnum-from-serial-number 77 "D" 3)
INFO:: Command: (insertion-code-from-serial-number 77 "D" 3)
INFO:: Command: (resname-from-serial-number 77 "D" 4)
INFO:: Command: (seqnum-from-serial-number 77 "D" 4)
INFO:: Command: (insertion-code-from-serial-number 77 "D" 4)
INFO:: Command: (does-residue-exist-p 77 D 1 )
INFO:: Command: (does-residue-exist-p 77 D 2 )
INFO:: Command: (does-residue-exist-p 77 D 3 )
INFO:: Command: (does-residue-exist-p 77 D 4 )
INFO:: Command: (does-residue-exist-p 77 D 5 )
INFO:: Command: (resname-from-serial-number 77 "E" 0)
INFO:: Command: (seqnum-from-serial-number 77 "E" 0)
INFO:: Command: (insertion-code-from-serial-number 77 "E" 0)
INFO:: Command: (resname-from-serial-number 77 "E" 1)
INFO:: Command: (seqnum-from-serial-number 77 "E" 1)
INFO:: Command: (insertion-code-from-serial-number 77 "E" 1)
INFO:: Command: (resname-from-serial-number 77 "E" 2)
INFO:: Command: (seqnum-from-serial-number 77 "E" 2)
INFO:: Command: (insertion-code-from-serial-number 77 "E" 2)
INFO:: Command: (resname-from-serial-number 77 "E" 3)
INFO:: Command: (seqnum-from-serial-number 77 "E" 3)
INFO:: Command: (insertion-code-from-serial-number 77 "E" 3)
INFO:: Command: (resname-from-serial-number 77 "E" 4)
INFO:: Command: (seqnum-from-serial-number 77 "E" 4)
INFO:: Command: (insertion-code-from-serial-number 77 "E" 4)
INFO:: Command: (does-residue-exist-p 77 E 1 )
INFO:: Command: (does-residue-exist-p 77 E 2 )
INFO:: Command: (does-residue-exist-p 77 E 3 )
INFO:: Command: (does-residue-exist-p 77 E 4 )
INFO:: Command: (does-residue-exist-p 77 E 5 )
INFO:: Command: (resname-from-serial-number 77 "F" 0)
INFO:: Command: (seqnum-from-serial-number 77 "F" 0)
INFO:: Command: (insertion-code-from-serial-number 77 "F" 0)
INFO:: Command: (resname-from-serial-number 77 "F" 1)
INFO:: Command: (seqnum-from-serial-number 77 "F" 1)
INFO:: Command: (insertion-code-from-serial-number 77 "F" 1)
INFO:: Command: (resname-from-serial-number 77 "F" 2)
INFO:: Command: (seqnum-from-serial-number 77 "F" 2)
INFO:: Command: (insertion-code-from-serial-number 77 "F" 2)
INFO:: Command: (resname-from-serial-number 77 "F" 3)
INFO:: Command: (seqnum-from-serial-number 77 "F" 3)
INFO:: Command: (insertion-code-from-serial-number 77 "F" 3)
INFO:: Command: (resname-from-serial-number 77 "F" 4)
INFO:: Command: (seqnum-from-serial-number 77 "F" 4)
INFO:: Command: (insertion-code-from-serial-number 77 "F" 4)
INFO:: Command: (does-residue-exist-p 77 F 1 )
INFO:: Command: (does-residue-exist-p 77 F 2 )
INFO:: Command: (does-residue-exist-p 77 F 3 )
INFO:: Command: (does-residue-exist-p 77 F 4 )
INFO:: Command: (does-residue-exist-p 77 F 5 )
INFO:: Command: (renumber-residue-range 77 "E" 1 5 5)
INFO:: Command: (renumber-residue-range 77 "F" 1 5 10)
INFO:: Command: (turn-on-backup 77)
INFO:: Command: (n-chains 77)
INFO:: Command: (chain_id 77 2)
INFO:: Command: (seqnum-from-serial-number 77 "D" 0)
INFO:: Command: (seqnum-from-serial-number 77 "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
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 78 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
Molecule 79 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
Molecule 80 read successfully
DEBUG:: there were 1 types with no dictionary 
-------- starting chain list -----------
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)
['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
INFO:: Command: (update-go-to-atom-window-on-new-mol)
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: (chain_id 78 5)
INFO:: Command: (chain_id 78 6)
INFO:: Command: (chain_id 78 7)
INFO:: Command: (chain_id 78 8)
INFO:: Command: (chain_id 78 9)
INFO:: Command: (chain_id 78 10)
INFO:: Command: (chain_id 78 11)
['A', 'B', 'C', 'D', '', 'E', 'F', 'G', 'H', 'I', 'J', 'K']
INFO:: Command: (write-pdb-file 78 "sym-merged.pdb")
ok
test53_0 (__main__.PdbMtzTestFunctions)
LSQ by atom ... INFO:: Command: (copy-molecule 0)
INFO:: Command: (copy-molecule 0)
INFO:: Matching/moving molecule number 83 to 82
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_Wed_Aug__2_00:51:40_2017_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
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 84 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
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 85 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 84 to 85
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_Wed_Aug__2_00:51:48_2017_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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 86 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:51:52_2017_modification_0.pdb.gz
INFO:: Command: (set-residue-name 86 "A" 37 "" "FRE")
INFO:: Command: (n-chains 86)
INFO:: Command: (chain_id 86 0)
INFO:: Command: (chain_id 86 1)
INFO:: Command: (seqnum-from-serial-number 86 "A" 0)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 0)
INFO:: Command: (seqnum-from-serial-number 86 "A" 1)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 1)
INFO:: Command: (seqnum-from-serial-number 86 "A" 2)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 2)
INFO:: Command: (seqnum-from-serial-number 86 "A" 3)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 3)
INFO:: Command: (seqnum-from-serial-number 86 "A" 4)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 4)
INFO:: Command: (seqnum-from-serial-number 86 "A" 5)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 5)
INFO:: Command: (seqnum-from-serial-number 86 "A" 6)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 6)
INFO:: Command: (seqnum-from-serial-number 86 "A" 7)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 7)
INFO:: Command: (seqnum-from-serial-number 86 "A" 8)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 8)
INFO:: Command: (seqnum-from-serial-number 86 "A" 9)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 9)
INFO:: Command: (seqnum-from-serial-number 86 "A" 10)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 10)
INFO:: Command: (seqnum-from-serial-number 86 "A" 11)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 11)
INFO:: Command: (seqnum-from-serial-number 86 "A" 12)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 12)
INFO:: Command: (seqnum-from-serial-number 86 "A" 13)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 13)
INFO:: Command: (seqnum-from-serial-number 86 "A" 14)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 14)
INFO:: Command: (seqnum-from-serial-number 86 "A" 15)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 15)
INFO:: Command: (seqnum-from-serial-number 86 "A" 16)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 16)
INFO:: Command: (seqnum-from-serial-number 86 "A" 17)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 17)
INFO:: Command: (seqnum-from-serial-number 86 "A" 18)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 18)
INFO:: Command: (seqnum-from-serial-number 86 "A" 19)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 19)
INFO:: Command: (seqnum-from-serial-number 86 "A" 20)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 20)
INFO:: Command: (seqnum-from-serial-number 86 "A" 21)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 21)
INFO:: Command: (seqnum-from-serial-number 86 "A" 22)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 22)
INFO:: Command: (seqnum-from-serial-number 86 "A" 23)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 23)
INFO:: Command: (seqnum-from-serial-number 86 "A" 24)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 24)
INFO:: Command: (seqnum-from-serial-number 86 "A" 25)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 25)
INFO:: Command: (seqnum-from-serial-number 86 "A" 26)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 26)
INFO:: Command: (seqnum-from-serial-number 86 "A" 27)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 27)
INFO:: Command: (seqnum-from-serial-number 86 "A" 28)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 28)
INFO:: Command: (seqnum-from-serial-number 86 "A" 29)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 29)
INFO:: Command: (seqnum-from-serial-number 86 "A" 30)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 30)
INFO:: Command: (seqnum-from-serial-number 86 "A" 31)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 31)
INFO:: Command: (seqnum-from-serial-number 86 "A" 32)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 32)
INFO:: Command: (seqnum-from-serial-number 86 "A" 33)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 33)
INFO:: Command: (seqnum-from-serial-number 86 "A" 34)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 34)
INFO:: Command: (seqnum-from-serial-number 86 "A" 35)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 35)
INFO:: Command: (seqnum-from-serial-number 86 "A" 36)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 36)
INFO:: Command: (seqnum-from-serial-number 86 "A" 37)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 37)
INFO:: Command: (seqnum-from-serial-number 86 "A" 38)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 38)
INFO:: Command: (seqnum-from-serial-number 86 "A" 39)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 39)
INFO:: Command: (seqnum-from-serial-number 86 "A" 40)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 40)
INFO:: Command: (seqnum-from-serial-number 86 "A" 41)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 41)
INFO:: Command: (seqnum-from-serial-number 86 "A" 42)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 42)
INFO:: Command: (seqnum-from-serial-number 86 "A" 43)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 43)
INFO:: Command: (seqnum-from-serial-number 86 "A" 44)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 44)
INFO:: Command: (seqnum-from-serial-number 86 "A" 45)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 45)
INFO:: Command: (seqnum-from-serial-number 86 "A" 46)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 46)
INFO:: Command: (seqnum-from-serial-number 86 "A" 47)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 47)
INFO:: Command: (seqnum-from-serial-number 86 "A" 48)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 48)
INFO:: Command: (seqnum-from-serial-number 86 "A" 49)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 49)
INFO:: Command: (seqnum-from-serial-number 86 "A" 50)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 50)
INFO:: Command: (seqnum-from-serial-number 86 "A" 51)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 51)
INFO:: Command: (seqnum-from-serial-number 86 "A" 52)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 52)
INFO:: Command: (seqnum-from-serial-number 86 "A" 53)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 53)
INFO:: Command: (seqnum-from-serial-number 86 "A" 54)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 54)
INFO:: Command: (seqnum-from-serial-number 86 "A" 55)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 55)
INFO:: Command: (seqnum-from-serial-number 86 "A" 56)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 56)
INFO:: Command: (seqnum-from-serial-number 86 "A" 57)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 57)
INFO:: Command: (seqnum-from-serial-number 86 "A" 58)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 58)
INFO:: Command: (seqnum-from-serial-number 86 "A" 59)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 59)
INFO:: Command: (seqnum-from-serial-number 86 "A" 60)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 60)
INFO:: Command: (seqnum-from-serial-number 86 "A" 61)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 61)
INFO:: Command: (seqnum-from-serial-number 86 "A" 62)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 62)
INFO:: Command: (seqnum-from-serial-number 86 "A" 63)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 63)
INFO:: Command: (seqnum-from-serial-number 86 "A" 64)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 64)
INFO:: Command: (seqnum-from-serial-number 86 "A" 65)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 65)
INFO:: Command: (seqnum-from-serial-number 86 "A" 66)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 66)
INFO:: Command: (seqnum-from-serial-number 86 "A" 67)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 67)
INFO:: Command: (seqnum-from-serial-number 86 "A" 68)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 68)
INFO:: Command: (seqnum-from-serial-number 86 "A" 69)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 69)
INFO:: Command: (seqnum-from-serial-number 86 "A" 70)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 70)
INFO:: Command: (seqnum-from-serial-number 86 "A" 71)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 71)
INFO:: Command: (seqnum-from-serial-number 86 "A" 72)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 72)
INFO:: Command: (seqnum-from-serial-number 86 "A" 73)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 73)
INFO:: Command: (seqnum-from-serial-number 86 "A" 74)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 74)
INFO:: Command: (seqnum-from-serial-number 86 "A" 75)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 75)
INFO:: Command: (seqnum-from-serial-number 86 "A" 76)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 76)
INFO:: Command: (seqnum-from-serial-number 86 "A" 77)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 77)
INFO:: Command: (seqnum-from-serial-number 86 "A" 78)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 78)
INFO:: Command: (seqnum-from-serial-number 86 "A" 79)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 79)
INFO:: Command: (seqnum-from-serial-number 86 "A" 80)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 80)
INFO:: Command: (seqnum-from-serial-number 86 "A" 81)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 81)
INFO:: Command: (seqnum-from-serial-number 86 "A" 82)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 82)
INFO:: Command: (seqnum-from-serial-number 86 "A" 83)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 83)
INFO:: Command: (seqnum-from-serial-number 86 "A" 84)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 84)
INFO:: Command: (seqnum-from-serial-number 86 "A" 85)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 85)
INFO:: Command: (seqnum-from-serial-number 86 "A" 86)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 86)
INFO:: Command: (seqnum-from-serial-number 86 "A" 87)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 87)
INFO:: Command: (seqnum-from-serial-number 86 "A" 88)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 88)
INFO:: Command: (seqnum-from-serial-number 86 "A" 89)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 89)
INFO:: Command: (seqnum-from-serial-number 86 "A" 90)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 90)
INFO:: Command: (seqnum-from-serial-number 86 "A" 91)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 91)
INFO:: Command: (seqnum-from-serial-number 86 "A" 92)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 92)
INFO:: Command: (seqnum-from-serial-number 86 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 0)
INFO:: Command: (seqnum-from-serial-number 86 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 1)
INFO:: Command: (seqnum-from-serial-number 86 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 2)
INFO:: Command: (seqnum-from-serial-number 86 "B" 3)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 3)
INFO:: Command: (seqnum-from-serial-number 86 "B" 4)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 4)
INFO:: Command: (seqnum-from-serial-number 86 "B" 5)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 5)
INFO:: Command: (seqnum-from-serial-number 86 "B" 6)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 6)
INFO:: Command: (seqnum-from-serial-number 86 "B" 7)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 7)
INFO:: Command: (seqnum-from-serial-number 86 "B" 8)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 8)
INFO:: Command: (seqnum-from-serial-number 86 "B" 9)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 9)
INFO:: Command: (seqnum-from-serial-number 86 "B" 10)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 10)
INFO:: Command: (seqnum-from-serial-number 86 "B" 11)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 11)
INFO:: Command: (seqnum-from-serial-number 86 "B" 12)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 12)
INFO:: Command: (seqnum-from-serial-number 86 "B" 13)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 13)
INFO:: Command: (seqnum-from-serial-number 86 "B" 14)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 14)
INFO:: Command: (seqnum-from-serial-number 86 "B" 15)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 15)
INFO:: Command: (seqnum-from-serial-number 86 "B" 16)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 16)
INFO:: Command: (seqnum-from-serial-number 86 "B" 17)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 17)
INFO:: Command: (seqnum-from-serial-number 86 "B" 18)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 18)
INFO:: Command: (seqnum-from-serial-number 86 "B" 19)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 19)
INFO:: Command: (seqnum-from-serial-number 86 "B" 20)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 20)
INFO:: Command: (seqnum-from-serial-number 86 "B" 21)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 21)
INFO:: Command: (seqnum-from-serial-number 86 "B" 22)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 22)
INFO:: Command: (seqnum-from-serial-number 86 "B" 23)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 23)
INFO:: Command: (seqnum-from-serial-number 86 "B" 24)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 24)
INFO:: Command: (seqnum-from-serial-number 86 "B" 25)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 25)
INFO:: Command: (seqnum-from-serial-number 86 "B" 26)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 26)
INFO:: Command: (seqnum-from-serial-number 86 "B" 27)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 27)
INFO:: Command: (seqnum-from-serial-number 86 "B" 28)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 28)
INFO:: Command: (seqnum-from-serial-number 86 "B" 29)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 29)
INFO:: Command: (seqnum-from-serial-number 86 "B" 30)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 30)
INFO:: Command: (seqnum-from-serial-number 86 "B" 31)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 31)
INFO:: Command: (seqnum-from-serial-number 86 "B" 32)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 32)
INFO:: Command: (seqnum-from-serial-number 86 "B" 33)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 33)
INFO:: Command: (seqnum-from-serial-number 86 "B" 34)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 34)
INFO:: Command: (seqnum-from-serial-number 86 "B" 35)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 35)
INFO:: Command: (seqnum-from-serial-number 86 "B" 36)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 36)
INFO:: Command: (seqnum-from-serial-number 86 "B" 37)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 37)
INFO:: Command: (seqnum-from-serial-number 86 "B" 38)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 38)
INFO:: Command: (seqnum-from-serial-number 86 "B" 39)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 39)
INFO:: Command: (seqnum-from-serial-number 86 "B" 40)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 40)
INFO:: Command: (seqnum-from-serial-number 86 "B" 41)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 41)
INFO:: Command: (seqnum-from-serial-number 86 "B" 42)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 42)
INFO:: Command: (seqnum-from-serial-number 86 "B" 43)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 43)
INFO:: Command: (seqnum-from-serial-number 86 "B" 44)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 44)
INFO:: Command: (seqnum-from-serial-number 86 "B" 45)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 45)
INFO:: Command: (seqnum-from-serial-number 86 "B" 46)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 46)
INFO:: Command: (seqnum-from-serial-number 86 "B" 47)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 47)
INFO:: Command: (seqnum-from-serial-number 86 "B" 48)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 48)
INFO:: Command: (seqnum-from-serial-number 86 "B" 49)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 49)
INFO:: Command: (seqnum-from-serial-number 86 "B" 50)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 50)
INFO:: Command: (seqnum-from-serial-number 86 "B" 51)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 51)
INFO:: Command: (seqnum-from-serial-number 86 "B" 52)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 52)
INFO:: Command: (seqnum-from-serial-number 86 "B" 53)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 53)
INFO:: Command: (seqnum-from-serial-number 86 "B" 54)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 54)
INFO:: Command: (seqnum-from-serial-number 86 "B" 55)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 55)
INFO:: Command: (seqnum-from-serial-number 86 "B" 56)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 56)
INFO:: Command: (seqnum-from-serial-number 86 "B" 57)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 57)
INFO:: Command: (seqnum-from-serial-number 86 "B" 58)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 58)
INFO:: Command: (seqnum-from-serial-number 86 "B" 59)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 59)
INFO:: Command: (seqnum-from-serial-number 86 "B" 60)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 60)
INFO:: Command: (seqnum-from-serial-number 86 "B" 61)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 61)
INFO:: Command: (seqnum-from-serial-number 86 "B" 62)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 62)
INFO:: Command: (seqnum-from-serial-number 86 "B" 63)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 63)
INFO:: Command: (seqnum-from-serial-number 86 "B" 64)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 64)
INFO:: Command: (seqnum-from-serial-number 86 "B" 65)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 65)
INFO:: Command: (seqnum-from-serial-number 86 "B" 66)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 66)
INFO:: Command: (seqnum-from-serial-number 86 "B" 67)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 67)
INFO:: Command: (seqnum-from-serial-number 86 "B" 68)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 68)
INFO:: Command: (seqnum-from-serial-number 86 "B" 69)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 69)
INFO:: Command: (seqnum-from-serial-number 86 "B" 70)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 70)
INFO:: Command: (seqnum-from-serial-number 86 "B" 71)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 71)
INFO:: Command: (seqnum-from-serial-number 86 "B" 72)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 72)
INFO:: Command: (seqnum-from-serial-number 86 "B" 73)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 73)
INFO:: Command: (seqnum-from-serial-number 86 "B" 74)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 74)
INFO:: Command: (seqnum-from-serial-number 86 "B" 75)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 75)
INFO:: Command: (seqnum-from-serial-number 86 "B" 76)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 76)
INFO:: Command: (seqnum-from-serial-number 86 "B" 77)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 77)
INFO:: Command: (seqnum-from-serial-number 86 "B" 78)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 78)
INFO:: Command: (seqnum-from-serial-number 86 "B" 79)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 79)
INFO:: Command: (seqnum-from-serial-number 86 "B" 80)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 80)
INFO:: Command: (seqnum-from-serial-number 86 "B" 81)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 81)
INFO:: Command: (seqnum-from-serial-number 86 "B" 82)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 82)
INFO:: Command: (seqnum-from-serial-number 86 "B" 83)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 83)
INFO:: Command: (seqnum-from-serial-number 86 "B" 84)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 84)
INFO:: Command: (seqnum-from-serial-number 86 "B" 85)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 85)
INFO:: Command: (seqnum-from-serial-number 86 "B" 86)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 86)
INFO:: Command: (seqnum-from-serial-number 86 "B" 87)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 87)
INFO:: Command: (seqnum-from-serial-number 86 "B" 88)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 88)
INFO:: Command: (seqnum-from-serial-number 86 "B" 89)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 89)
INFO:: Command: (seqnum-from-serial-number 86 "B" 90)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 90)
INFO:: Command: (seqnum-from-serial-number 86 "B" 91)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 91)
INFO:: Command: (seqnum-from-serial-number 86 "B" 92)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 92)
INFO:: Command: (seqnum-from-serial-number 86 "B" 93)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 93)
INFO:: Command: (seqnum-from-serial-number 86 "B" 94)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 94)
INFO:: Command: (seqnum-from-serial-number 86 "B" 95)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 95)
INFO:: Command: (n-chains 86)
INFO:: Command: (chain_id 86 0)
INFO:: Command: (chain_id 86 1)
INFO:: Command: (seqnum-from-serial-number 86 "A" 0)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 0)
INFO:: Command: (seqnum-from-serial-number 86 "A" 1)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 1)
INFO:: Command: (seqnum-from-serial-number 86 "A" 2)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 2)
INFO:: Command: (seqnum-from-serial-number 86 "A" 3)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 3)
INFO:: Command: (seqnum-from-serial-number 86 "A" 4)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 4)
INFO:: Command: (seqnum-from-serial-number 86 "A" 5)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 5)
INFO:: Command: (seqnum-from-serial-number 86 "A" 6)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 6)
INFO:: Command: (seqnum-from-serial-number 86 "A" 7)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 7)
INFO:: Command: (seqnum-from-serial-number 86 "A" 8)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 8)
INFO:: Command: (seqnum-from-serial-number 86 "A" 9)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 9)
INFO:: Command: (seqnum-from-serial-number 86 "A" 10)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 10)
INFO:: Command: (seqnum-from-serial-number 86 "A" 11)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 11)
INFO:: Command: (seqnum-from-serial-number 86 "A" 12)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 12)
INFO:: Command: (seqnum-from-serial-number 86 "A" 13)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 13)
INFO:: Command: (seqnum-from-serial-number 86 "A" 14)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 14)
INFO:: Command: (seqnum-from-serial-number 86 "A" 15)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 15)
INFO:: Command: (seqnum-from-serial-number 86 "A" 16)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 16)
INFO:: Command: (seqnum-from-serial-number 86 "A" 17)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 17)
INFO:: Command: (seqnum-from-serial-number 86 "A" 18)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 18)
INFO:: Command: (seqnum-from-serial-number 86 "A" 19)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 19)
INFO:: Command: (seqnum-from-serial-number 86 "A" 20)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 20)
INFO:: Command: (seqnum-from-serial-number 86 "A" 21)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 21)
INFO:: Command: (seqnum-from-serial-number 86 "A" 22)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 22)
INFO:: Command: (seqnum-from-serial-number 86 "A" 23)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 23)
INFO:: Command: (seqnum-from-serial-number 86 "A" 24)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 24)
INFO:: Command: (seqnum-from-serial-number 86 "A" 25)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 25)
INFO:: Command: (seqnum-from-serial-number 86 "A" 26)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 26)
INFO:: Command: (seqnum-from-serial-number 86 "A" 27)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 27)
INFO:: Command: (seqnum-from-serial-number 86 "A" 28)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 28)
INFO:: Command: (seqnum-from-serial-number 86 "A" 29)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 29)
INFO:: Command: (seqnum-from-serial-number 86 "A" 30)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 30)
INFO:: Command: (seqnum-from-serial-number 86 "A" 31)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 31)
INFO:: Command: (seqnum-from-serial-number 86 "A" 32)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 32)
INFO:: Command: (seqnum-from-serial-number 86 "A" 33)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 33)
INFO:: Command: (seqnum-from-serial-number 86 "A" 34)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 34)
INFO:: Command: (seqnum-from-serial-number 86 "A" 35)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 35)
INFO:: Command: (seqnum-from-serial-number 86 "A" 36)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 36)
INFO:: Command: (seqnum-from-serial-number 86 "A" 37)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 37)
INFO:: Command: (seqnum-from-serial-number 86 "A" 38)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 38)
INFO:: Command: (seqnum-from-serial-number 86 "A" 39)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 39)
INFO:: Command: (seqnum-from-serial-number 86 "A" 40)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 40)
INFO:: Command: (seqnum-from-serial-number 86 "A" 41)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 41)
INFO:: Command: (seqnum-from-serial-number 86 "A" 42)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 42)
INFO:: Command: (seqnum-from-serial-number 86 "A" 43)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 43)
INFO:: Command: (seqnum-from-serial-number 86 "A" 44)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 44)
INFO:: Command: (seqnum-from-serial-number 86 "A" 45)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 45)
INFO:: Command: (seqnum-from-serial-number 86 "A" 46)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 46)
INFO:: Command: (seqnum-from-serial-number 86 "A" 47)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 47)
INFO:: Command: (seqnum-from-serial-number 86 "A" 48)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 48)
INFO:: Command: (seqnum-from-serial-number 86 "A" 49)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 49)
INFO:: Command: (seqnum-from-serial-number 86 "A" 50)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 50)
INFO:: Command: (seqnum-from-serial-number 86 "A" 51)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 51)
INFO:: Command: (seqnum-from-serial-number 86 "A" 52)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 52)
INFO:: Command: (seqnum-from-serial-number 86 "A" 53)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 53)
INFO:: Command: (seqnum-from-serial-number 86 "A" 54)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 54)
INFO:: Command: (seqnum-from-serial-number 86 "A" 55)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 55)
INFO:: Command: (seqnum-from-serial-number 86 "A" 56)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 56)
INFO:: Command: (seqnum-from-serial-number 86 "A" 57)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 57)
INFO:: Command: (seqnum-from-serial-number 86 "A" 58)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 58)
INFO:: Command: (seqnum-from-serial-number 86 "A" 59)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 59)
INFO:: Command: (seqnum-from-serial-number 86 "A" 60)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 60)
INFO:: Command: (seqnum-from-serial-number 86 "A" 61)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 61)
INFO:: Command: (seqnum-from-serial-number 86 "A" 62)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 62)
INFO:: Command: (seqnum-from-serial-number 86 "A" 63)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 63)
INFO:: Command: (seqnum-from-serial-number 86 "A" 64)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 64)
INFO:: Command: (seqnum-from-serial-number 86 "A" 65)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 65)
INFO:: Command: (seqnum-from-serial-number 86 "A" 66)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 66)
INFO:: Command: (seqnum-from-serial-number 86 "A" 67)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 67)
INFO:: Command: (seqnum-from-serial-number 86 "A" 68)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 68)
INFO:: Command: (seqnum-from-serial-number 86 "A" 69)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 69)
INFO:: Command: (seqnum-from-serial-number 86 "A" 70)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 70)
INFO:: Command: (seqnum-from-serial-number 86 "A" 71)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 71)
INFO:: Command: (seqnum-from-serial-number 86 "A" 72)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 72)
INFO:: Command: (seqnum-from-serial-number 86 "A" 73)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 73)
INFO:: Command: (seqnum-from-serial-number 86 "A" 74)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 74)
INFO:: Command: (seqnum-from-serial-number 86 "A" 75)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 75)
INFO:: Command: (seqnum-from-serial-number 86 "A" 76)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 76)
INFO:: Command: (seqnum-from-serial-number 86 "A" 77)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 77)
INFO:: Command: (seqnum-from-serial-number 86 "A" 78)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 78)
INFO:: Command: (seqnum-from-serial-number 86 "A" 79)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 79)
INFO:: Command: (seqnum-from-serial-number 86 "A" 80)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 80)
INFO:: Command: (seqnum-from-serial-number 86 "A" 81)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 81)
INFO:: Command: (seqnum-from-serial-number 86 "A" 82)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 82)
INFO:: Command: (seqnum-from-serial-number 86 "A" 83)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 83)
INFO:: Command: (seqnum-from-serial-number 86 "A" 84)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 84)
INFO:: Command: (seqnum-from-serial-number 86 "A" 85)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 85)
INFO:: Command: (seqnum-from-serial-number 86 "A" 86)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 86)
INFO:: Command: (seqnum-from-serial-number 86 "A" 87)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 87)
INFO:: Command: (seqnum-from-serial-number 86 "A" 88)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 88)
INFO:: Command: (seqnum-from-serial-number 86 "A" 89)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 89)
INFO:: Command: (seqnum-from-serial-number 86 "A" 90)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 90)
INFO:: Command: (seqnum-from-serial-number 86 "A" 91)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 91)
INFO:: Command: (seqnum-from-serial-number 86 "A" 92)
INFO:: Command: (insertion-code-from-serial-number 86 "A" 92)
INFO:: Command: (seqnum-from-serial-number 86 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 0)
INFO:: Command: (seqnum-from-serial-number 86 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 1)
INFO:: Command: (seqnum-from-serial-number 86 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 2)
INFO:: Command: (seqnum-from-serial-number 86 "B" 3)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 3)
INFO:: Command: (seqnum-from-serial-number 86 "B" 4)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 4)
INFO:: Command: (seqnum-from-serial-number 86 "B" 5)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 5)
INFO:: Command: (seqnum-from-serial-number 86 "B" 6)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 6)
INFO:: Command: (seqnum-from-serial-number 86 "B" 7)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 7)
INFO:: Command: (seqnum-from-serial-number 86 "B" 8)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 8)
INFO:: Command: (seqnum-from-serial-number 86 "B" 9)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 9)
INFO:: Command: (seqnum-from-serial-number 86 "B" 10)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 10)
INFO:: Command: (seqnum-from-serial-number 86 "B" 11)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 11)
INFO:: Command: (seqnum-from-serial-number 86 "B" 12)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 12)
INFO:: Command: (seqnum-from-serial-number 86 "B" 13)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 13)
INFO:: Command: (seqnum-from-serial-number 86 "B" 14)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 14)
INFO:: Command: (seqnum-from-serial-number 86 "B" 15)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 15)
INFO:: Command: (seqnum-from-serial-number 86 "B" 16)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 16)
INFO:: Command: (seqnum-from-serial-number 86 "B" 17)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 17)
INFO:: Command: (seqnum-from-serial-number 86 "B" 18)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 18)
INFO:: Command: (seqnum-from-serial-number 86 "B" 19)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 19)
INFO:: Command: (seqnum-from-serial-number 86 "B" 20)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 20)
INFO:: Command: (seqnum-from-serial-number 86 "B" 21)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 21)
INFO:: Command: (seqnum-from-serial-number 86 "B" 22)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 22)
INFO:: Command: (seqnum-from-serial-number 86 "B" 23)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 23)
INFO:: Command: (seqnum-from-serial-number 86 "B" 24)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 24)
INFO:: Command: (seqnum-from-serial-number 86 "B" 25)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 25)
INFO:: Command: (seqnum-from-serial-number 86 "B" 26)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 26)
INFO:: Command: (seqnum-from-serial-number 86 "B" 27)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 27)
INFO:: Command: (seqnum-from-serial-number 86 "B" 28)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 28)
INFO:: Command: (seqnum-from-serial-number 86 "B" 29)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 29)
INFO:: Command: (seqnum-from-serial-number 86 "B" 30)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 30)
INFO:: Command: (seqnum-from-serial-number 86 "B" 31)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 31)
INFO:: Command: (seqnum-from-serial-number 86 "B" 32)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 32)
INFO:: Command: (seqnum-from-serial-number 86 "B" 33)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 33)
INFO:: Command: (seqnum-from-serial-number 86 "B" 34)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 34)
INFO:: Command: (seqnum-from-serial-number 86 "B" 35)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 35)
INFO:: Command: (seqnum-from-serial-number 86 "B" 36)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 36)
INFO:: Command: (seqnum-from-serial-number 86 "B" 37)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 37)
INFO:: Command: (seqnum-from-serial-number 86 "B" 38)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 38)
INFO:: Command: (seqnum-from-serial-number 86 "B" 39)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 39)
INFO:: Command: (seqnum-from-serial-number 86 "B" 40)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 40)
INFO:: Command: (seqnum-from-serial-number 86 "B" 41)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 41)
INFO:: Command: (seqnum-from-serial-number 86 "B" 42)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 42)
INFO:: Command: (seqnum-from-serial-number 86 "B" 43)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 43)
INFO:: Command: (seqnum-from-serial-number 86 "B" 44)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 44)
INFO:: Command: (seqnum-from-serial-number 86 "B" 45)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 45)
INFO:: Command: (seqnum-from-serial-number 86 "B" 46)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 46)
INFO:: Command: (seqnum-from-serial-number 86 "B" 47)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 47)
INFO:: Command: (seqnum-from-serial-number 86 "B" 48)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 48)
INFO:: Command: (seqnum-from-serial-number 86 "B" 49)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 49)
INFO:: Command: (seqnum-from-serial-number 86 "B" 50)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 50)
INFO:: Command: (seqnum-from-serial-number 86 "B" 51)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 51)
INFO:: Command: (seqnum-from-serial-number 86 "B" 52)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 52)
INFO:: Command: (seqnum-from-serial-number 86 "B" 53)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 53)
INFO:: Command: (seqnum-from-serial-number 86 "B" 54)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 54)
INFO:: Command: (seqnum-from-serial-number 86 "B" 55)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 55)
INFO:: Command: (seqnum-from-serial-number 86 "B" 56)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 56)
INFO:: Command: (seqnum-from-serial-number 86 "B" 57)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 57)
INFO:: Command: (seqnum-from-serial-number 86 "B" 58)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 58)
INFO:: Command: (seqnum-from-serial-number 86 "B" 59)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 59)
INFO:: Command: (seqnum-from-serial-number 86 "B" 60)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 60)
INFO:: Command: (seqnum-from-serial-number 86 "B" 61)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 61)
INFO:: Command: (seqnum-from-serial-number 86 "B" 62)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 62)
INFO:: Command: (seqnum-from-serial-number 86 "B" 63)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 63)
INFO:: Command: (seqnum-from-serial-number 86 "B" 64)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 64)
INFO:: Command: (seqnum-from-serial-number 86 "B" 65)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 65)
INFO:: Command: (seqnum-from-serial-number 86 "B" 66)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 66)
INFO:: Command: (seqnum-from-serial-number 86 "B" 67)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 67)
INFO:: Command: (seqnum-from-serial-number 86 "B" 68)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 68)
INFO:: Command: (seqnum-from-serial-number 86 "B" 69)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 69)
INFO:: Command: (seqnum-from-serial-number 86 "B" 70)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 70)
INFO:: Command: (seqnum-from-serial-number 86 "B" 71)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 71)
INFO:: Command: (seqnum-from-serial-number 86 "B" 72)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 72)
INFO:: Command: (seqnum-from-serial-number 86 "B" 73)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 73)
INFO:: Command: (seqnum-from-serial-number 86 "B" 74)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 74)
INFO:: Command: (seqnum-from-serial-number 86 "B" 75)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 75)
INFO:: Command: (seqnum-from-serial-number 86 "B" 76)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 76)
INFO:: Command: (seqnum-from-serial-number 86 "B" 77)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 77)
INFO:: Command: (seqnum-from-serial-number 86 "B" 78)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 78)
INFO:: Command: (seqnum-from-serial-number 86 "B" 79)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 79)
INFO:: Command: (seqnum-from-serial-number 86 "B" 80)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 80)
INFO:: Command: (seqnum-from-serial-number 86 "B" 81)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 81)
INFO:: Command: (seqnum-from-serial-number 86 "B" 82)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 82)
INFO:: Command: (seqnum-from-serial-number 86 "B" 83)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 83)
INFO:: Command: (seqnum-from-serial-number 86 "B" 84)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 84)
INFO:: Command: (seqnum-from-serial-number 86 "B" 85)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 85)
INFO:: Command: (seqnum-from-serial-number 86 "B" 86)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 86)
INFO:: Command: (seqnum-from-serial-number 86 "B" 87)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 87)
INFO:: Command: (seqnum-from-serial-number 86 "B" 88)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 88)
INFO:: Command: (seqnum-from-serial-number 86 "B" 89)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 89)
INFO:: Command: (seqnum-from-serial-number 86 "B" 90)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 90)
INFO:: Command: (seqnum-from-serial-number 86 "B" 91)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 91)
INFO:: Command: (seqnum-from-serial-number 86 "B" 92)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 92)
INFO:: Command: (seqnum-from-serial-number 86 "B" 93)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 93)
INFO:: Command: (seqnum-from-serial-number 86 "B" 94)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 94)
INFO:: Command: (seqnum-from-serial-number 86 "B" 95)
INFO:: Command: (insertion-code-from-serial-number 86 "B" 95)
0 [86, 'A', 1, '']
1 [86, 'A', 2, '']
2 [86, 'A', 3, '']
3 [86, 'A', 4, '']
4 [86, 'A', 5, '']
5 [86, 'A', 6, '']
6 [86, 'A', 7, '']
7 [86, 'A', 8, '']
8 [86, 'A', 9, '']
9 [86, 'A', 10, '']
10 [86, 'A', 11, '']
11 [86, 'A', 12, '']
12 [86, 'A', 13, '']
13 [86, 'A', 14, '']
14 [86, 'A', 15, '']
15 [86, 'A', 16, '']
16 [86, 'A', 17, '']
17 [86, 'A', 18, '']
18 [86, 'A', 19, '']
19 [86, 'A', 20, '']
20 [86, 'A', 21, '']
21 [86, 'A', 22, '']
22 [86, 'A', 23, '']
23 [86, 'A', 24, '']
24 [86, 'A', 25, '']
25 [86, 'A', 26, '']
26 [86, 'A', 27, '']
27 [86, 'A', 28, '']
28 [86, 'A', 29, '']
29 [86, 'A', 30, '']
30 [86, 'A', 31, '']
31 [86, 'A', 32, '']
32 [86, 'A', 33, '']
33 [86, 'A', 34, '']
34 [86, 'A', 35, '']
35 [86, 'A', 36, '']
36 [86, 'A', 37, '']
36 [86, 'A', 37, '']
37 [86, 'A', 38, '']
38 [86, 'A', 39, '']
39 [86, 'A', 40, '']
40 [86, 'A', 41, '']
41 [86, 'A', 42, '']
42 [86, 'A', 43, '']
43 [86, 'A', 44, '']
44 [86, 'A', 45, '']
45 [86, 'A', 46, '']
46 [86, 'A', 47, '']
47 [86, 'A', 48, '']
48 [86, 'A', 49, '']
49 [86, 'A', 50, '']
50 [86, 'A', 51, '']
51 [86, 'A', 52, '']
52 [86, 'A', 53, '']
53 [86, 'A', 54, '']
54 [86, 'A', 55, '']
55 [86, 'A', 56, '']
56 [86, 'A', 57, '']
57 [86, 'A', 58, '']
58 [86, 'A', 59, '']
59 [86, 'A', 60, '']
60 [86, 'A', 61, '']
61 [86, 'A', 62, '']
62 [86, 'A', 63, '']
63 [86, 'A', 64, '']
64 [86, 'A', 65, '']
65 [86, 'A', 66, '']
66 [86, 'A', 67, '']
67 [86, 'A', 68, '']
68 [86, 'A', 69, '']
69 [86, 'A', 70, '']
70 [86, 'A', 71, '']
71 [86, 'A', 72, '']
72 [86, 'A', 73, '']
73 [86, 'A', 74, '']
74 [86, 'A', 75, '']
75 [86, 'A', 76, '']
76 [86, 'A', 77, '']
77 [86, 'A', 78, '']
78 [86, 'A', 79, '']
79 [86, 'A', 80, '']
80 [86, 'A', 81, '']
81 [86, 'A', 82, '']
82 [86, 'A', 83, '']
83 [86, 'A', 84, '']
84 [86, 'A', 85, '']
85 [86, 'A', 86, '']
86 [86, 'A', 87, '']
87 [86, 'A', 88, '']
88 [86, 'A', 89, '']
89 [86, 'A', 90, '']
90 [86, 'A', 91, '']
91 [86, 'A', 92, '']
92 [86, 'A', 93, '']
93 [86, 'B', 1, '']
94 [86, 'B', 2, '']
95 [86, 'B', 3, '']
96 [86, 'B', 4, '']
97 [86, 'B', 5, '']
98 [86, 'B', 6, '']
99 [86, 'B', 7, '']
100 [86, 'B', 8, '']
101 [86, 'B', 9, '']
102 [86, 'B', 10, '']
103 [86, 'B', 11, '']
104 [86, 'B', 12, '']
105 [86, 'B', 13, '']
106 [86, 'B', 14, '']
107 [86, 'B', 15, '']
108 [86, 'B', 16, '']
109 [86, 'B', 17, '']
110 [86, 'B', 18, '']
111 [86, 'B', 19, '']
112 [86, 'B', 20, '']
113 [86, 'B', 21, '']
114 [86, 'B', 22, '']
115 [86, 'B', 23, '']
116 [86, 'B', 24, '']
117 [86, 'B', 25, '']
118 [86, 'B', 26, '']
119 [86, 'B', 27, '']
120 [86, 'B', 28, '']
121 [86, 'B', 29, '']
122 [86, 'B', 30, '']
123 [86, 'B', 31, '']
124 [86, 'B', 32, '']
125 [86, 'B', 33, '']
126 [86, 'B', 34, '']
127 [86, 'B', 35, '']
128 [86, 'B', 36, '']
129 [86, 'B', 37, '']
130 [86, 'B', 38, '']
131 [86, 'B', 39, '']
132 [86, 'B', 40, '']
133 [86, 'B', 41, '']
134 [86, 'B', 42, '']
135 [86, 'B', 43, '']
136 [86, 'B', 44, '']
137 [86, 'B', 45, '']
138 [86, 'B', 46, '']
139 [86, 'B', 47, '']
140 [86, 'B', 48, '']
141 [86, 'B', 49, '']
142 [86, 'B', 50, '']
143 [86, 'B', 51, '']
144 [86, 'B', 52, '']
145 [86, 'B', 53, '']
146 [86, 'B', 54, '']
147 [86, 'B', 55, '']
148 [86, 'B', 56, '']
149 [86, 'B', 57, '']
150 [86, 'B', 58, '']
151 [86, 'B', 59, '']
152 [86, 'B', 60, '']
153 [86, 'B', 61, '']
154 [86, 'B', 62, '']
155 [86, 'B', 63, '']
156 [86, 'B', 64, '']
157 [86, 'B', 65, '']
158 [86, 'B', 66, '']
159 [86, 'B', 67, '']
160 [86, 'B', 68, '']
161 [86, 'B', 69, '']
162 [86, 'B', 70, '']
163 [86, 'B', 71, '']
164 [86, 'B', 72, '']
165 [86, 'B', 73, '']
166 [86, 'B', 74, '']
167 [86, 'B', 75, '']
168 [86, 'B', 76, '']
169 [86, 'B', 77, '']
170 [86, 'B', 78, '']
171 [86, 'B', 79, '']
172 [86, 'B', 80, '']
173 [86, 'B', 81, '']
174 [86, 'B', 82, '']
175 [86, 'B', 83, '']
176 [86, 'B', 84, '']
177 [86, 'B', 85, '']
178 [86, 'B', 86, '']
179 [86, 'B', 87, '']
180 [86, 'B', 88, '']
181 [86, 'B', 89, '']
182 [86, 'B', 90, '']
183 [86, 'B', 91, '']
184 [86, 'B', 92, '']
185 [86, 'B', 93, '']
186 [86, 'B', 94, '']
187 [86, 'B', 95, '']
188 [86, '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
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:: Command: (n-chains 87)
INFO:: Command: (chain_id 87 0)
INFO:: Command: (chain_id 87 1)
INFO:: Command: (seqnum-from-serial-number 87 "A" 0)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 0)
INFO:: Command: (seqnum-from-serial-number 87 "A" 1)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 1)
INFO:: Command: (seqnum-from-serial-number 87 "A" 2)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 2)
INFO:: Command: (seqnum-from-serial-number 87 "A" 3)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 3)
INFO:: Command: (seqnum-from-serial-number 87 "A" 4)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 4)
INFO:: Command: (seqnum-from-serial-number 87 "A" 5)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 5)
INFO:: Command: (seqnum-from-serial-number 87 "A" 6)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 6)
INFO:: Command: (seqnum-from-serial-number 87 "A" 7)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 7)
INFO:: Command: (seqnum-from-serial-number 87 "A" 8)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 8)
INFO:: Command: (seqnum-from-serial-number 87 "A" 9)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 9)
INFO:: Command: (seqnum-from-serial-number 87 "A" 10)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 10)
INFO:: Command: (seqnum-from-serial-number 87 "A" 11)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 11)
INFO:: Command: (seqnum-from-serial-number 87 "A" 12)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 12)
INFO:: Command: (seqnum-from-serial-number 87 "A" 13)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 13)
INFO:: Command: (seqnum-from-serial-number 87 "A" 14)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 14)
INFO:: Command: (seqnum-from-serial-number 87 "A" 15)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 15)
INFO:: Command: (seqnum-from-serial-number 87 "A" 16)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 16)
INFO:: Command: (seqnum-from-serial-number 87 "A" 17)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 17)
INFO:: Command: (seqnum-from-serial-number 87 "A" 18)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 18)
INFO:: Command: (seqnum-from-serial-number 87 "A" 19)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 19)
INFO:: Command: (seqnum-from-serial-number 87 "A" 20)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 20)
INFO:: Command: (seqnum-from-serial-number 87 "A" 21)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 21)
INFO:: Command: (seqnum-from-serial-number 87 "A" 22)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 22)
INFO:: Command: (seqnum-from-serial-number 87 "A" 23)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 23)
INFO:: Command: (seqnum-from-serial-number 87 "A" 24)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 24)
INFO:: Command: (seqnum-from-serial-number 87 "A" 25)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 25)
INFO:: Command: (seqnum-from-serial-number 87 "A" 26)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 26)
INFO:: Command: (seqnum-from-serial-number 87 "A" 27)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 27)
INFO:: Command: (seqnum-from-serial-number 87 "A" 28)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 28)
INFO:: Command: (seqnum-from-serial-number 87 "A" 29)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 29)
INFO:: Command: (seqnum-from-serial-number 87 "A" 30)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 30)
INFO:: Command: (seqnum-from-serial-number 87 "A" 31)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 31)
INFO:: Command: (seqnum-from-serial-number 87 "A" 32)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 32)
INFO:: Command: (seqnum-from-serial-number 87 "A" 33)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 33)
INFO:: Command: (seqnum-from-serial-number 87 "A" 34)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 34)
INFO:: Command: (seqnum-from-serial-number 87 "A" 35)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 35)
INFO:: Command: (seqnum-from-serial-number 87 "A" 36)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 36)
INFO:: Command: (seqnum-from-serial-number 87 "A" 37)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 37)
INFO:: Command: (seqnum-from-serial-number 87 "A" 38)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 38)
INFO:: Command: (seqnum-from-serial-number 87 "A" 39)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 39)
INFO:: Command: (seqnum-from-serial-number 87 "A" 40)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 40)
INFO:: Command: (seqnum-from-serial-number 87 "A" 41)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 41)
INFO:: Command: (seqnum-from-serial-number 87 "A" 42)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 42)
INFO:: Command: (seqnum-from-serial-number 87 "A" 43)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 43)
INFO:: Command: (seqnum-from-serial-number 87 "A" 44)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 44)
INFO:: Command: (seqnum-from-serial-number 87 "A" 45)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 45)
INFO:: Command: (seqnum-from-serial-number 87 "A" 46)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 46)
INFO:: Command: (seqnum-from-serial-number 87 "A" 47)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 47)
INFO:: Command: (seqnum-from-serial-number 87 "A" 48)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 48)
INFO:: Command: (seqnum-from-serial-number 87 "A" 49)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 49)
INFO:: Command: (seqnum-from-serial-number 87 "A" 50)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 50)
INFO:: Command: (seqnum-from-serial-number 87 "A" 51)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 51)
INFO:: Command: (seqnum-from-serial-number 87 "A" 52)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 52)
INFO:: Command: (seqnum-from-serial-number 87 "A" 53)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 53)
INFO:: Command: (seqnum-from-serial-number 87 "A" 54)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 54)
INFO:: Command: (seqnum-from-serial-number 87 "A" 55)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 55)
INFO:: Command: (seqnum-from-serial-number 87 "A" 56)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 56)
INFO:: Command: (seqnum-from-serial-number 87 "A" 57)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 57)
INFO:: Command: (seqnum-from-serial-number 87 "A" 58)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 58)
INFO:: Command: (seqnum-from-serial-number 87 "A" 59)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 59)
INFO:: Command: (seqnum-from-serial-number 87 "A" 60)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 60)
INFO:: Command: (seqnum-from-serial-number 87 "A" 61)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 61)
INFO:: Command: (seqnum-from-serial-number 87 "A" 62)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 62)
INFO:: Command: (seqnum-from-serial-number 87 "A" 63)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 63)
INFO:: Command: (seqnum-from-serial-number 87 "A" 64)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 64)
INFO:: Command: (seqnum-from-serial-number 87 "A" 65)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 65)
INFO:: Command: (seqnum-from-serial-number 87 "A" 66)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 66)
INFO:: Command: (seqnum-from-serial-number 87 "A" 67)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 67)
INFO:: Command: (seqnum-from-serial-number 87 "A" 68)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 68)
INFO:: Command: (seqnum-from-serial-number 87 "A" 69)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 69)
INFO:: Command: (seqnum-from-serial-number 87 "A" 70)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 70)
INFO:: Command: (seqnum-from-serial-number 87 "A" 71)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 71)
INFO:: Command: (seqnum-from-serial-number 87 "A" 72)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 72)
INFO:: Command: (seqnum-from-serial-number 87 "A" 73)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 73)
INFO:: Command: (seqnum-from-serial-number 87 "A" 74)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 74)
INFO:: Command: (seqnum-from-serial-number 87 "A" 75)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 75)
INFO:: Command: (seqnum-from-serial-number 87 "A" 76)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 76)
INFO:: Command: (seqnum-from-serial-number 87 "A" 77)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 77)
INFO:: Command: (seqnum-from-serial-number 87 "A" 78)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 78)
INFO:: Command: (seqnum-from-serial-number 87 "A" 79)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 79)
INFO:: Command: (seqnum-from-serial-number 87 "A" 80)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 80)
INFO:: Command: (seqnum-from-serial-number 87 "A" 81)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 81)
INFO:: Command: (seqnum-from-serial-number 87 "A" 82)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 82)
INFO:: Command: (seqnum-from-serial-number 87 "A" 83)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 83)
INFO:: Command: (seqnum-from-serial-number 87 "A" 84)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 84)
INFO:: Command: (seqnum-from-serial-number 87 "A" 85)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 85)
INFO:: Command: (seqnum-from-serial-number 87 "A" 86)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 86)
INFO:: Command: (seqnum-from-serial-number 87 "A" 87)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 87)
INFO:: Command: (seqnum-from-serial-number 87 "A" 88)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 88)
INFO:: Command: (seqnum-from-serial-number 87 "A" 89)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 89)
INFO:: Command: (seqnum-from-serial-number 87 "A" 90)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 90)
INFO:: Command: (seqnum-from-serial-number 87 "A" 91)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 91)
INFO:: Command: (seqnum-from-serial-number 87 "A" 92)
INFO:: Command: (insertion-code-from-serial-number 87 "A" 92)
INFO:: Command: (seqnum-from-serial-number 87 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 0)
INFO:: Command: (seqnum-from-serial-number 87 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 1)
INFO:: Command: (seqnum-from-serial-number 87 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 2)
INFO:: Command: (seqnum-from-serial-number 87 "B" 3)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 3)
INFO:: Command: (seqnum-from-serial-number 87 "B" 4)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 4)
INFO:: Command: (seqnum-from-serial-number 87 "B" 5)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 5)
INFO:: Command: (seqnum-from-serial-number 87 "B" 6)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 6)
INFO:: Command: (seqnum-from-serial-number 87 "B" 7)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 7)
INFO:: Command: (seqnum-from-serial-number 87 "B" 8)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 8)
INFO:: Command: (seqnum-from-serial-number 87 "B" 9)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 9)
INFO:: Command: (seqnum-from-serial-number 87 "B" 10)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 10)
INFO:: Command: (seqnum-from-serial-number 87 "B" 11)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 11)
INFO:: Command: (seqnum-from-serial-number 87 "B" 12)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 12)
INFO:: Command: (seqnum-from-serial-number 87 "B" 13)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 13)
INFO:: Command: (seqnum-from-serial-number 87 "B" 14)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 14)
INFO:: Command: (seqnum-from-serial-number 87 "B" 15)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 15)
INFO:: Command: (seqnum-from-serial-number 87 "B" 16)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 16)
INFO:: Command: (seqnum-from-serial-number 87 "B" 17)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 17)
INFO:: Command: (seqnum-from-serial-number 87 "B" 18)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 18)
INFO:: Command: (seqnum-from-serial-number 87 "B" 19)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 19)
INFO:: Command: (seqnum-from-serial-number 87 "B" 20)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 20)
INFO:: Command: (seqnum-from-serial-number 87 "B" 21)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 21)
INFO:: Command: (seqnum-from-serial-number 87 "B" 22)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 22)
INFO:: Command: (seqnum-from-serial-number 87 "B" 23)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 23)
INFO:: Command: (seqnum-from-serial-number 87 "B" 24)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 24)
INFO:: Command: (seqnum-from-serial-number 87 "B" 25)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 25)
INFO:: Command: (seqnum-from-serial-number 87 "B" 26)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 26)
INFO:: Command: (seqnum-from-serial-number 87 "B" 27)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 27)
INFO:: Command: (seqnum-from-serial-number 87 "B" 28)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 28)
INFO:: Command: (seqnum-from-serial-number 87 "B" 29)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 29)
INFO:: Command: (seqnum-from-serial-number 87 "B" 30)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 30)
INFO:: Command: (seqnum-from-serial-number 87 "B" 31)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 31)
INFO:: Command: (seqnum-from-serial-number 87 "B" 32)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 32)
INFO:: Command: (seqnum-from-serial-number 87 "B" 33)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 33)
INFO:: Command: (seqnum-from-serial-number 87 "B" 34)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 34)
INFO:: Command: (seqnum-from-serial-number 87 "B" 35)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 35)
INFO:: Command: (seqnum-from-serial-number 87 "B" 36)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 36)
INFO:: Command: (seqnum-from-serial-number 87 "B" 37)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 37)
INFO:: Command: (seqnum-from-serial-number 87 "B" 38)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 38)
INFO:: Command: (seqnum-from-serial-number 87 "B" 39)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 39)
INFO:: Command: (seqnum-from-serial-number 87 "B" 40)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 40)
INFO:: Command: (seqnum-from-serial-number 87 "B" 41)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 41)
INFO:: Command: (seqnum-from-serial-number 87 "B" 42)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 42)
INFO:: Command: (seqnum-from-serial-number 87 "B" 43)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 43)
INFO:: Command: (seqnum-from-serial-number 87 "B" 44)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 44)
INFO:: Command: (seqnum-from-serial-number 87 "B" 45)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 45)
INFO:: Command: (seqnum-from-serial-number 87 "B" 46)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 46)
INFO:: Command: (seqnum-from-serial-number 87 "B" 47)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 47)
INFO:: Command: (seqnum-from-serial-number 87 "B" 48)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 48)
INFO:: Command: (seqnum-from-serial-number 87 "B" 49)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 49)
INFO:: Command: (seqnum-from-serial-number 87 "B" 50)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 50)
INFO:: Command: (seqnum-from-serial-number 87 "B" 51)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 51)
INFO:: Command: (seqnum-from-serial-number 87 "B" 52)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 52)
INFO:: Command: (seqnum-from-serial-number 87 "B" 53)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 53)
INFO:: Command: (seqnum-from-serial-number 87 "B" 54)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 54)
INFO:: Command: (seqnum-from-serial-number 87 "B" 55)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 55)
INFO:: Command: (seqnum-from-serial-number 87 "B" 56)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 56)
INFO:: Command: (seqnum-from-serial-number 87 "B" 57)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 57)
INFO:: Command: (seqnum-from-serial-number 87 "B" 58)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 58)
INFO:: Command: (seqnum-from-serial-number 87 "B" 59)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 59)
INFO:: Command: (seqnum-from-serial-number 87 "B" 60)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 60)
INFO:: Command: (seqnum-from-serial-number 87 "B" 61)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 61)
INFO:: Command: (seqnum-from-serial-number 87 "B" 62)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 62)
INFO:: Command: (seqnum-from-serial-number 87 "B" 63)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 63)
INFO:: Command: (seqnum-from-serial-number 87 "B" 64)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 64)
INFO:: Command: (seqnum-from-serial-number 87 "B" 65)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 65)
INFO:: Command: (seqnum-from-serial-number 87 "B" 66)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 66)
INFO:: Command: (seqnum-from-serial-number 87 "B" 67)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 67)
INFO:: Command: (seqnum-from-serial-number 87 "B" 68)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 68)
INFO:: Command: (seqnum-from-serial-number 87 "B" 69)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 69)
INFO:: Command: (seqnum-from-serial-number 87 "B" 70)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 70)
INFO:: Command: (seqnum-from-serial-number 87 "B" 71)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 71)
INFO:: Command: (seqnum-from-serial-number 87 "B" 72)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 72)
INFO:: Command: (seqnum-from-serial-number 87 "B" 73)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 73)
INFO:: Command: (seqnum-from-serial-number 87 "B" 74)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 74)
INFO:: Command: (seqnum-from-serial-number 87 "B" 75)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 75)
INFO:: Command: (seqnum-from-serial-number 87 "B" 76)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 76)
INFO:: Command: (seqnum-from-serial-number 87 "B" 77)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 77)
INFO:: Command: (seqnum-from-serial-number 87 "B" 78)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 78)
INFO:: Command: (seqnum-from-serial-number 87 "B" 79)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 79)
INFO:: Command: (seqnum-from-serial-number 87 "B" 80)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 80)
INFO:: Command: (seqnum-from-serial-number 87 "B" 81)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 81)
INFO:: Command: (seqnum-from-serial-number 87 "B" 82)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 82)
INFO:: Command: (seqnum-from-serial-number 87 "B" 83)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 83)
INFO:: Command: (seqnum-from-serial-number 87 "B" 84)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 84)
INFO:: Command: (seqnum-from-serial-number 87 "B" 85)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 85)
INFO:: Command: (seqnum-from-serial-number 87 "B" 86)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 86)
INFO:: Command: (seqnum-from-serial-number 87 "B" 87)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 87)
INFO:: Command: (seqnum-from-serial-number 87 "B" 88)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 88)
INFO:: Command: (seqnum-from-serial-number 87 "B" 89)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 89)
INFO:: Command: (seqnum-from-serial-number 87 "B" 90)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 90)
INFO:: Command: (seqnum-from-serial-number 87 "B" 91)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 91)
INFO:: Command: (seqnum-from-serial-number 87 "B" 92)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 92)
INFO:: Command: (seqnum-from-serial-number 87 "B" 93)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 93)
INFO:: Command: (seqnum-from-serial-number 87 "B" 94)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 94)
INFO:: Command: (seqnum-from-serial-number 87 "B" 95)
INFO:: Command: (insertion-code-from-serial-number 87 "B" 95)
   specs: 189 [[87, 'A', 1, ''], [87, 'A', 2, ''], [87, 'A', 3, ''], [87, 'A', 4, ''], [87, 'A', 5, ''], [87, 'A', 6, ''], [87, 'A', 7, ''], [87, 'A', 8, ''], [87, 'A', 9, ''], [87, 'A', 10, ''], [87, 'A', 11, ''], [87, 'A', 12, ''], [87, 'A', 13, ''], [87, 'A', 14, ''], [87, 'A', 15, ''], [87, 'A', 16, ''], [87, 'A', 17, ''], [87, 'A', 18, ''], [87, 'A', 19, ''], [87, 'A', 20, ''], [87, 'A', 21, ''], [87, 'A', 22, ''], [87, 'A', 23, ''], [87, 'A', 24, ''], [87, 'A', 25, ''], [87, 'A', 26, ''], [87, 'A', 27, ''], [87, 'A', 28, ''], [87, 'A', 29, ''], [87, 'A', 30, ''], [87, 'A', 31, ''], [87, 'A', 32, ''], [87, 'A', 33, ''], [87, 'A', 34, ''], [87, 'A', 35, ''], [87, 'A', 36, ''], [87, 'A', 37, ''], [87, 'A', 38, ''], [87, 'A', 39, ''], [87, 'A', 40, ''], [87, 'A', 41, ''], [87, 'A', 42, ''], [87, 'A', 43, ''], [87, 'A', 44, ''], [87, 'A', 45, ''], [87, 'A', 46, ''], [87, 'A', 47, ''], [87, 'A', 48, ''], [87, 'A', 49, ''], [87, 'A', 50, ''], [87, 'A', 51, ''], [87, 'A', 52, ''], [87, 'A', 53, ''], [87, 'A', 54, ''], [87, 'A', 55, ''], [87, 'A', 56, ''], [87, 'A', 57, ''], [87, 'A', 58, ''], [87, 'A', 59, ''], [87, 'A', 60, ''], [87, 'A', 61, ''], [87, 'A', 62, ''], [87, 'A', 63, ''], [87, 'A', 64, ''], [87, 'A', 65, ''], [87, 'A', 66, ''], [87, 'A', 67, ''], [87, 'A', 68, ''], [87, 'A', 69, ''], [87, 'A', 70, ''], [87, 'A', 71, ''], [87, 'A', 72, ''], [87, 'A', 73, ''], [87, 'A', 74, ''], [87, 'A', 75, ''], [87, 'A', 76, ''], [87, 'A', 77, ''], [87, 'A', 78, ''], [87, 'A', 79, ''], [87, 'A', 80, ''], [87, 'A', 81, ''], [87, 'A', 82, ''], [87, 'A', 83, ''], [87, 'A', 84, ''], [87, 'A', 85, ''], [87, 'A', 86, ''], [87, 'A', 87, ''], [87, 'A', 88, ''], [87, 'A', 89, ''], [87, 'A', 90, ''], [87, 'A', 91, ''], [87, 'A', 92, ''], [87, 'A', 93, ''], [87, 'B', 1, ''], [87, 'B', 2, ''], [87, 'B', 3, ''], [87, 'B', 4, ''], [87, 'B', 5, ''], [87, 'B', 6, ''], [87, 'B', 7, ''], [87, 'B', 8, ''], [87, 'B', 9, ''], [87, 'B', 10, ''], [87, 'B', 11, ''], [87, 'B', 12, ''], [87, 'B', 13, ''], [87, 'B', 14, ''], [87, 'B', 15, ''], [87, 'B', 16, ''], [87, 'B', 17, ''], [87, 'B', 18, ''], [87, 'B', 19, ''], [87, 'B', 20, ''], [87, 'B', 21, ''], [87, 'B', 22, ''], [87, 'B', 23, ''], [87, 'B', 24, ''], [87, 'B', 25, ''], [87, 'B', 26, ''], [87, 'B', 27, ''], [87, 'B', 28, ''], [87, 'B', 29, ''], [87, 'B', 30, ''], [87, 'B', 31, ''], [87, 'B', 32, ''], [87, 'B', 33, ''], [87, 'B', 34, ''], [87, 'B', 35, ''], [87, 'B', 36, ''], [87, 'B', 37, ''], [87, 'B', 38, ''], [87, 'B', 39, ''], [87, 'B', 40, ''], [87, 'B', 41, ''], [87, 'B', 42, ''], [87, 'B', 43, ''], [87, 'B', 44, ''], [87, 'B', 45, ''], [87, 'B', 46, ''], [87, 'B', 47, ''], [87, 'B', 48, ''], [87, 'B', 49, ''], [87, 'B', 50, ''], [87, 'B', 51, ''], [87, 'B', 52, ''], [87, 'B', 53, ''], [87, 'B', 54, ''], [87, 'B', 55, ''], [87, 'B', 56, ''], [87, 'B', 57, ''], [87, 'B', 58, ''], [87, 'B', 59, ''], [87, 'B', 60, ''], [87, 'B', 61, ''], [87, 'B', 62, ''], [87, 'B', 63, ''], [87, 'B', 64, ''], [87, 'B', 65, ''], [87, 'B', 66, ''], [87, 'B', 67, ''], [87, 'B', 68, ''], [87, 'B', 69, ''], [87, 'B', 70, ''], [87, 'B', 71, ''], [87, 'B', 72, ''], [87, 'B', 73, ''], [87, 'B', 74, ''], [87, 'B', 75, ''], [87, 'B', 76, ''], [87, 'B', 77, ''], [87, 'B', 78, ''], [87, 'B', 79, ''], [87, 'B', 80, ''], [87, 'B', 81, ''], [87, 'B', 82, ''], [87, 'B', 83, ''], [87, 'B', 84, ''], [87, 'B', 85, ''], [87, 'B', 86, ''], [87, 'B', 87, ''], [87, 'B', 88, ''], [87, 'B', 89, ''], [87, 'B', 90, ''], [87, 'B', 91, ''], [87, 'B', 92, ''], [87, 'B', 93, ''], [87, 'B', 94, ''], [87, 'B', 95, ''], [87, '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
INFO:: NCS chain comparison 10/85
Molecule 88 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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 89 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: found bad VAL chiral atom: A 2   CB  
ok
test62_0 (__main__.PdbMtzTestFunctions)
Fix for Oliver Clarke fit by atom selection bug ... 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
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:: 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:: 0.036 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.016 seconds for FFT
INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.875045   max: 2.97757
INFO:: 0.004 seconds for statistics
      Map mean: ........ 1.05439e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.106 seconds for contour map
INFO:: 0.162 seconds in total
masking....masking done
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:10_2017_modification_0.pdb.gz
INFO:: replace_coords: 745 atoms updated.
bl: 0.0363730669589
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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 92 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_0.pdb.gz
INFO:: Command: (renumber-residue-range 92 "A" 10 20 -55)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_1.pdb.gz
INFO:: Command: (renumber-residue-range 92 "A" 90 93 10)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_2.pdb.gz
INFO:: Command: (renumber-residue-range 92 "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 92 "A" 80 91 12)
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:52:14_2017_modification_3.pdb.gz
INFO:: Command: (renumber-residue-range 92 "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 93 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 94 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 95 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/insulin.res")
reject uvw = (  58,  41,  76) rho: 6.07907 implausible (high)
INFO:: Map statistics: mean: -7.57023e-05 st.d: 0.304925
INFO:: Map statistics:  min: -0.781031   max: 5.15441
Map statistics: mean: -7.57023e-05 st.d: 0.304925
Map statistics: min: -0.781031, max: 5.15441
 -0.706838    129
 -0.558452    2336
 -0.410066    14093
  -0.26168    33222
 -0.113294    65572
 0.0350918    78739
  0.183478    27967
  0.331864    6373
   0.48025    3664
  0.628636    2583
  0.777022    2083
  0.925408    1626
   1.07379    1370
   1.22218    1012
   1.37057    757
   1.51895    523
   1.66734    337
   1.81572    250
   1.96411    158
    2.1125    95
   2.26088    75
   2.40927    54
   2.55765    42
   2.70604    15
   2.85442    14
   3.00281    15
    3.1512    7
   3.29958    7
   3.44797    7
   3.59635    1
   3.74474    1
   3.89313    7
   4.04151    4
    4.1899    3
   4.33828    3
   4.48667    0
   4.63506    2
   4.78344    1
   4.93183    1
   5.08021    1
    5.2286    0
INFO:: Map statistics: mean: -1.00548e-05 st.d: 0.0468085
INFO:: Map statistics:  min: -0.211523   max: 0.648623
Map statistics: mean: -1.00548e-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
 0.0572724    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 ... 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 ... 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
WARNING:: No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/atom_selection_from_insulin.res_Wed_Aug__2_00:52:16_2017_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 99 "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_Wed_Aug__2_00:52:16_2017_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 95 "D" 68)
INFO:: Command: (seqnum-from-serial-number 95 "D" 68)
INFO:: Command: (insertion-code-from-serial-number 95 "D" 68)
ok
test08_0 (__main__.ShelxTestFunctions)
Find Waters for a SHELXL molecule ... INFO:: Command: (n-chains 95)
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 0.304925
INFO:: Using density cut-off: 0.182955 (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 = (    -4.856,      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,     8.133,     53.25) 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_Wed_Aug__2_00:52:16_2017_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 95)
INFO:: Command: (resname-from-serial-number 95 "D" 96)
INFO:: Command: (seqnum-from-serial-number 95 "D" 96)
INFO:: Command: (insertion-code-from-serial-number 95 "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 100 read successfully
INFO:: Command: (read-shelx-ins-file "/lmb/home/pemsley/data/greg-data/miller/shelx-test4-NPD-mini.res")
INFO:: Command: (close-molecule 100)
ok
test10_0 (__main__.ShelxTestFunctions)
close shelx molecules ... INFO:: Command: (close-molecule 96)
INFO:: Command: (close-molecule 95)
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 101 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 102 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 103 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 104 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
Molecule 105 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_Wed_Aug__2_00:52:16_2017_modification_0.pdb.gz
::: add_cif_dictionary() called with coot-ccp4/libcheck_3GP.cif -999999 0
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:16_2017_modification_1.pdb.gz
INFO:: Command: (delete-residue-hydrogens 105 "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
Molecule 106 read successfully
DEBUG:: there were 0 types with no dictionary 
here 1
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_monomer-3GP.pdb_Wed_Aug__2_00:52:20_2017_modification_0.pdb.gz
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
WARNING:: 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 
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
WARNING:: No Symmetry for this model
Molecule 108 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_Wed_Aug__2_00:52:16_2017_modification_2.pdb.gz
INFO:: Command: (backup-state 105)
INFO:: Command: (turn-off-backup 105)
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: Command: (turn-on-backup 105)
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
Molecule 109 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (copy-molecule 109)
INFO:: Command: (copy-molecule 109)
INFO:: Command: (copy-molecule 109)
INFO:: Command: (copy-molecule 109)
INFO:: Command: (copy-molecule 109)
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
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 115 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:: 0.145 seconds to read MTZ file
INFO:: 0.097 seconds to initialize map
INFO:: 0.066 seconds for FFT
INFO:: Map statistics: mean: -8.79003e-07 st.d: 0.171188
INFO:: Map statistics:  min: -0.695441   max: 1.34304
INFO:: 0.021 seconds for statistics
      Map mean: ........ -8.79003e-07
      Map sigma: ....... 0.171188
      Map maximum: ..... 1.34304
      Map minimum: ..... -0.695441
INFO:: 0.04 seconds for contour map
INFO:: 0.369 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:: 0.093 seconds to read MTZ file
INFO:: 0.002 seconds to initialize map
INFO:: 0.067 seconds for FFT
INFO:: Map statistics: mean: 2.0939e-06 st.d: 0.0333923
INFO:: Map statistics:  min: -0.191665   max: 0.366077
INFO:: 0.021 seconds for statistics
      Map mean: ........ 2.0939e-06
      Map sigma: ....... 0.0333923
      Map maximum: ..... 0.366077
      Map minimum: ..... -0.191665
INFO:: 0.015 seconds for contour map
INFO:: 0.198 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 109   with wiggly flag: 0
in execute_ligand_search_internal() import maps from mol 116
INFO:: Protein centre at: xyz = (     58.29,     34.65,     30.63)
INFO:: Map statistics: mean: -0.0216745 st.d: 0.0886263
INFO:: Map statistics:  min: -0.695441   max: 0.754209
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
-0.0612189    102888
-0.0249776    143000
 0.0112636    471775
 0.0475049    106846
 0.0837461    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    6
   0.77233    1
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
------------ 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
------------ 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
------------ 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
------------ 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
------------ 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
------------ 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
------------ 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
------------ 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
------------ 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
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
   Fitting NPO gave these results:  [119, 120, 121, 122, 123, 124, 125, 126, 127, 128]
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
Molecule 129 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Command: (copy-molecule 129)
INFO:: Command: (set-go-to-atom-molecule 129)
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:53_2017_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_Wed_Aug__2_00:52:53_2017_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:53_2017_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_Aug__2_00:52:53_2017_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
WARNING:: No Symmetry for this model
Molecule 131 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 ... ::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif -999999 0
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
::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif -999999 0
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
::: add_cif_dictionary() called with /lmb/home/pemsley/data/greg-data/libcheck_3GP.cif -999999 0
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
test11_0 (__main__.LigandTestFunctions)
pyrogen dictionary does not make double-quoted atom names ... 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
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 132 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 132
INFO:: Command: (assign-pir-sequence 132 "A" ">test

ACDEFGHIKLMNPQ*")
debug seq ACDEFGHIKLMNPQ
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 132
INFO:: Command: (assign-pir-sequence 132 "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
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 133 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:: 0.026 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.013 seconds for FFT
INFO:: Map statistics: mean: 1.05439e-09 st.d: 0.311501
INFO:: Map statistics:  min: -0.875045   max: 2.97757
INFO:: 0.004 seconds for statistics
      Map mean: ........ 1.05439e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.076 seconds for contour map
INFO:: 0.119 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 133
INFO:: Command: (assign-pir-sequence 133 "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 133 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_Wed_Aug__2_00:53:07_2017_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
WARNING:: No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_Aug__2_00:53:08_2017_modification_0.pdb.gz
INFO:: Command: (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: Command: (copy-molecule 135)
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 136)
INFO:: Command: (chain_id 136 0)
INFO:: Command: (chain_id 136 1)
INFO:: Command: (is-solvent-chain-p 136 "A")
   There are 8 residues in chain A
INFO:: Command: (resname-from-serial-number 136 "A" 0)
INFO:: Command: (seqnum-from-serial-number 136 "A" 0)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 0)
INFO:: Command: (resname-from-serial-number 136 "A" 1)
INFO:: Command: (seqnum-from-serial-number 136 "A" 1)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 1)
INFO:: Command: (resname-from-serial-number 136 "A" 2)
INFO:: Command: (seqnum-from-serial-number 136 "A" 2)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 2)
INFO:: Command: (resname-from-serial-number 136 "A" 3)
INFO:: Command: (seqnum-from-serial-number 136 "A" 3)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 3)
INFO:: Command: (resname-from-serial-number 136 "A" 4)
INFO:: Command: (seqnum-from-serial-number 136 "A" 4)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 4)
INFO:: Command: (resname-from-serial-number 136 "A" 5)
INFO:: Command: (seqnum-from-serial-number 136 "A" 5)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 5)
INFO:: Command: (resname-from-serial-number 136 "A" 6)
INFO:: Command: (seqnum-from-serial-number 136 "A" 6)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 6)
INFO:: Command: (resname-from-serial-number 136 "A" 7)
INFO:: Command: (seqnum-from-serial-number 136 "A" 7)
INFO:: Command: (insertion-code-from-serial-number 136 "A" 7)
INFO:: Command: (is-solvent-chain-p 136 "B")
   There are 8 residues in chain B
INFO:: Command: (resname-from-serial-number 136 "B" 0)
INFO:: Command: (seqnum-from-serial-number 136 "B" 0)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 0)
INFO:: Command: (resname-from-serial-number 136 "B" 1)
INFO:: Command: (seqnum-from-serial-number 136 "B" 1)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 1)
INFO:: Command: (resname-from-serial-number 136 "B" 2)
INFO:: Command: (seqnum-from-serial-number 136 "B" 2)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 2)
INFO:: Command: (resname-from-serial-number 136 "B" 3)
INFO:: Command: (seqnum-from-serial-number 136 "B" 3)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 3)
INFO:: Command: (resname-from-serial-number 136 "B" 4)
INFO:: Command: (seqnum-from-serial-number 136 "B" 4)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 4)
INFO:: Command: (resname-from-serial-number 136 "B" 5)
INFO:: Command: (seqnum-from-serial-number 136 "B" 5)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 5)
INFO:: Command: (resname-from-serial-number 136 "B" 6)
INFO:: Command: (seqnum-from-serial-number 136 "B" 6)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 6)
INFO:: Command: (resname-from-serial-number 136 "B" 7)
INFO:: Command: (seqnum-from-serial-number 136 "B" 7)
INFO:: Command: (insertion-code-from-serial-number 136 "B" 7)
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: Command: (copy-molecule 135)
INFO:: Matching/moving molecule number 137 to 137
INFO:: LSQ matched 125 atoms
INFO:: 125 matched atoms had: 
   mean devi: 2.32709e-06
    rms devi: 2.52247e-06
    max devi: 4.32529e-06
    min devi: 5.02443e-07
INFO:: Axis orientation: (   -0.2821,  -0.09945,    0.9542)
INFO:: Rotation in CCP4 Polar Angles: Polar = (     0,     0,     0)
INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Wed_Aug__2_00:53:12_2017_modification_0.pdb.gz
INFO:: coordinates transformed by orthogonal matrix: 
|         1,-2.361e-08,-2.461e-09|
| 2.361e-08,         1, 6.979e-09|
| 2.461e-09,-6.979e-09,         1|
(    -24.01,    -24.01,    -24.01)
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
Molecule 138 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
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 139 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 138)
INFO:: Command: (graphics-to-ca-plus-ligands-representation 139)
INFO:: reference 138 has 750 atoms selected
INFO:: moving    139 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_Wed_Aug__2_00:53:20_2017_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/pdb2qc1-sans-cho.pdb
    49    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 50)
    50    /lmb/home/pemsley/data/greg-data/monomer-VAL.pdb
INFO:: Command: (molecule-name 51)
    51    /lmb/home/pemsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb
INFO:: Command: (molecule-name 52)
    52    atom selection from tutorial-modern.pdb
INFO:: Command: (molecule-name 53)
    53    /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
INFO:: Command: (molecule-name 54)
    54    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 55)
    55    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 56)
    56    atom selection from tutorial-modern.pdb
INFO:: Command: (molecule-name 57)
    57    /lmb/home/pemsley/data/greg-data/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/rnase-A-needs-an-insertion.pdb
INFO:: Command: (molecule-name 60)
    60    /lmb/home/pemsley/data/greg-data/tutorial-modern.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/pdb3hfl.ent
    63    /lmb/home/pemsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT
INFO:: Command: (molecule-name 64)
    64    Ideal-A-form-RNA
INFO:: Command: (molecule-name 65)
    65    Ideal-A-form-RNA
INFO:: Command: (molecule-name 66)
    66    Ideal-A-form-DNA
INFO:: Command: (molecule-name 67)
    67    Ideal-A-form-DNA
INFO:: Command: (molecule-name 68)
    68    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 69)
    69    /lmb/home/pemsley/data/greg-data/some-waters-with-ter.pdb
INFO:: Command: (molecule-name 70)
    70    /lmb/home/pemsley/data/greg-data/tm+some-waters.pdb
INFO:: Command: (molecule-name 71)
    71    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 72)
    72    /lmb/home/pemsley/data/greg-data/water-test-no-cell.pdb
INFO:: Command: (molecule-name 73)
    73    /lmb/home/pemsley/data/greg-data/pathological-water-test.pdb
INFO:: Command: (molecule-name 74)
    74    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
    75    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 76)
    76    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 77)
    77    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 78)
    78    /lmb/home/pemsley/data/greg-data/pdb1hvv.ent
INFO:: Command: (molecule-name 79)
    79    /lmb/home/pemsley/data/greg-data/monomer-ACT.pdb
INFO:: Command: (molecule-name 80)
    80    /lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 81)
    81    SymOp_-X,-X+Y,-Z+1/3_Copy_of_78
INFO:: Command: (molecule-name 82)
    82    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 83)
    83    Copy_of_/lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 84)
    84    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 85)
    85    /lmb/home/pemsley/data/greg-data/pdb1py3.ent
INFO:: Command: (molecule-name 86)
    86    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
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/2goz-manip.pdb
INFO:: Command: (molecule-name 89)
    89    rnase_zip_test.pdb.gz
INFO:: Command: (molecule-name 90)
    90    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
    91    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 92)
    92    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 93)
    93    /lmb/home/pemsley/data/greg-data/HOF.RES
INFO:: Command: (molecule-name 94)
    94    /lmb/home/pemsley/data/greg-data/hollander.ins
    97    /lmb/home/pemsley/data/greg-data/insulin.fcf Diff-SigmaA
INFO:: Command: (molecule-name 98)
    98    atom selection from insulin.res
INFO:: Command: (molecule-name 99)
    99    atom selection from insulin.res
INFO:: Command: (molecule-name 101)
    101    /lmb/home/pemsley/data/greg-data/horma-p21.res
INFO:: Command: (molecule-name 102)
    102    new-horma.ins
INFO:: Command: (molecule-name 103)
    103    /lmb/home/pemsley/data/greg-data/crash.hat
INFO:: Command: (molecule-name 104)
    104    /lmb/home/pemsley/data/greg-data/crash.hat
INFO:: Command: (molecule-name 105)
    105    coot-ccp4/monomer-3GP.pdb
INFO:: Command: (molecule-name 106)
    106    /lmb/home/pemsley/data/greg-data/monomer-3GP.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/test-LIG.pdb
INFO:: Command: (molecule-name 109)
    109    /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    Copy_of_/lmb/home/pemsley/data/greg-data/monomer-NPO.pdb
INFO:: Command: (molecule-name 115)
    115    /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
    116    /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT
    117    /lmb/home/pemsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT
    118    Masked (by protein)
INFO:: Command: (molecule-name 119)
    119    Fitted ligand #0-0
INFO:: Command: (molecule-name 120)
    120    Fitted ligand #1-0
INFO:: Command: (molecule-name 121)
    121    Fitted ligand #2-0
INFO:: Command: (molecule-name 122)
    122    Fitted ligand #3-0
INFO:: Command: (molecule-name 123)
    123    Fitted ligand #4-0
INFO:: Command: (molecule-name 124)
    124    Fitted ligand #5-0
INFO:: Command: (molecule-name 125)
    125    Fitted ligand #6-0
INFO:: Command: (molecule-name 126)
    126    Fitted ligand #7-0
INFO:: Command: (molecule-name 127)
    127    Fitted ligand #8-0
INFO:: Command: (molecule-name 128)
    128    Fitted ligand #9-0
INFO:: Command: (molecule-name 129)
    129    coot-ccp4/monomer-3GP.pdb
INFO:: Command: (molecule-name 130)
    130    Copy_of_coot-ccp4/monomer-3GP.pdb
INFO:: Command: (molecule-name 131)
    131    /lmb/home/pemsley/data/greg-data/dipole-residues.pdb
INFO:: Command: (molecule-name 132)
    132    /lmb/home/pemsley/data/greg-data/tutorial-modern.pdb
INFO:: Command: (molecule-name 133)
    133    /lmb/home/pemsley/data/greg-data/crashes_on_cootaneering-v2.pdb
    134    /lmb/home/pemsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT
INFO:: Command: (molecule-name 135)
    135    Ideal-A-form-RNA
INFO:: Command: (molecule-name 136)
    136    Copy_of_Ideal-A-form-RNA
INFO:: Command: (molecule-name 137)
    137    Copy_of_Ideal-A-form-RNA
INFO:: Command: (molecule-name 138)
    138    /lmb/home/pemsley/data/greg-data/1wly.pdb
INFO:: Command: (molecule-name 139)
    139    /lmb/home/pemsley/data/greg-data/1yb5.pdb
INFO:: Command: (graphics-to-ca-plus-ligands-representation 139)
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
Molecule 140 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
INFO:: NCS chain comparison 0/337
Molecule 141 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: reference 140 has 169 atoms selected
INFO:: moving    141 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_Wed_Aug__2_00:53:31_2017_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:: 0.0260 seconds to read MTZ file
INFO:: 0.0000 seconds to initialize map
INFO:: 0.0130 seconds for FFT
INFO:: Map statistics: mean: 0.0000 st.d: 0.3115
INFO:: Map statistics:  min: -0.8750   max: 2.9776
INFO:: 0.0040 seconds for statistics
      Map mean: ........ 0.0000
      Map sigma: ....... 0.3115
      Map maximum: ..... 2.9776
      Map minimum: ..... -0.8750
INFO:: 0.0770 seconds for contour map
INFO:: 0.1200 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:: 737280 out of 737280 (100.0000%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
INFO:: Map statistics: mean: 0.0003 st.d: 0.3250
INFO:: Map statistics:  min: -1.4894   max: 2.4019
Map statistics: mean: 0.0003 st.d: 0.3250
Map statistics: min: -1.4894, max: 2.4019
   -1.4407    3
   -1.3435    7
   -1.2462    16
   -1.1489    7
   -1.0516    17
   -0.9543    61
   -0.8570    255
   -0.7598    907
   -0.6625    3123
   -0.5652    9819
   -0.4679    26025
   -0.3706    54787
   -0.2733    87759
   -0.1761    106866
   -0.0788    105275
    0.0185    88484
    0.1158    67330
    0.2131    50443
    0.3103    38437
    0.4076    28654
    0.5049    21003
    0.6022    15144
    0.6995    10724
    0.7968    7514
    0.8940    5100
    0.9913    3555
    1.0886    2282
    1.1859    1498
    1.2832    914
    1.3804    569
    1.4777    316
    1.5750    169
    1.6723    84
    1.7696    44
    1.8669    35
    1.9641    30
    2.0614    9
    2.1587    9
    2.2560    2
    2.3533    3
    2.4506    1
INFO:: installing ghost map with name :Map 142 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)
INFO:: Map statistics: mean: 0.0004 st.d: 0.3236
INFO:: Map statistics:  min: -1.4496   max: 2.3411
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    1
    2.3885    1
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 147 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
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 148 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_0.pdb.gz
INFO:: Command: (delete-residue 148 "B" 1 "")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_1.pdb.gz
INFO:: Command: (delete-residue 148 "B" 2 "")
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_2.pdb.gz
INFO:: Command: (delete-residue 148 "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: 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 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_Wed_Aug__2_00:53:39_2017_modification_3.pdb.gz
INFO:: Command: (seqnum-from-serial-number 148 "B" 0)
INFO:: Command: (seqnum-from-serial-number 148 "B" 1)
INFO:: Command: (seqnum-from-serial-number 148 "B" 2)
INFO:: Command: (seqnum-from-serial-number 148 "B" 3)
INFO:: Command: (seqnum-from-serial-number 148 "B" 4)
INFO:: Command: (seqnum-from-serial-number 148 "B" 5)
INFO:: Command: (seqnum-from-serial-number 148 "B" 6)
INFO:: Command: (seqnum-from-serial-number 148 "B" 7)
INFO:: Command: (seqnum-from-serial-number 148 "B" 8)
INFO:: Command: (seqnum-from-serial-number 148 "B" 9)
INFO:: Command: (seqnum-from-serial-number 148 "B" 10)
INFO:: Command: (seqnum-from-serial-number 148 "B" 11)
INFO:: Command: (seqnum-from-serial-number 148 "B" 12)
INFO:: Command: (seqnum-from-serial-number 148 "B" 13)
INFO:: Command: (seqnum-from-serial-number 148 "B" 14)
INFO:: Command: (seqnum-from-serial-number 148 "B" 15)
INFO:: Command: (seqnum-from-serial-number 148 "B" 16)
INFO:: Command: (seqnum-from-serial-number 148 "B" 17)
INFO:: Command: (seqnum-from-serial-number 148 "B" 18)
INFO:: Command: (seqnum-from-serial-number 148 "B" 19)
INFO:: Command: (seqnum-from-serial-number 148 "B" 20)
INFO:: Command: (seqnum-from-serial-number 148 "B" 21)
INFO:: Command: (seqnum-from-serial-number 148 "B" 22)
INFO:: Command: (seqnum-from-serial-number 148 "B" 23)
INFO:: Command: (seqnum-from-serial-number 148 "B" 24)
INFO:: Command: (seqnum-from-serial-number 148 "B" 25)
INFO:: Command: (seqnum-from-serial-number 148 "B" 26)
INFO:: Command: (seqnum-from-serial-number 148 "B" 27)
INFO:: Command: (seqnum-from-serial-number 148 "B" 28)
INFO:: Command: (seqnum-from-serial-number 148 "B" 29)
INFO:: Command: (seqnum-from-serial-number 148 "B" 30)
INFO:: Command: (seqnum-from-serial-number 148 "B" 31)
INFO:: Command: (seqnum-from-serial-number 148 "B" 32)
INFO:: Command: (seqnum-from-serial-number 148 "B" 33)
INFO:: Command: (seqnum-from-serial-number 148 "B" 34)
INFO:: Command: (seqnum-from-serial-number 148 "B" 35)
INFO:: Command: (seqnum-from-serial-number 148 "B" 36)
INFO:: Command: (seqnum-from-serial-number 148 "B" 37)
INFO:: Command: (seqnum-from-serial-number 148 "B" 38)
INFO:: Command: (seqnum-from-serial-number 148 "B" 39)
INFO:: Command: (seqnum-from-serial-number 148 "B" 40)
INFO:: Command: (seqnum-from-serial-number 148 "B" 41)
INFO:: Command: (seqnum-from-serial-number 148 "B" 42)
INFO:: Command: (seqnum-from-serial-number 148 "B" 43)
INFO:: Command: (seqnum-from-serial-number 148 "B" 44)
INFO:: Command: (seqnum-from-serial-number 148 "B" 45)
INFO:: Command: (seqnum-from-serial-number 148 "B" 46)
INFO:: Command: (seqnum-from-serial-number 148 "B" 47)
INFO:: Command: (seqnum-from-serial-number 148 "B" 48)
INFO:: Command: (seqnum-from-serial-number 148 "B" 49)
INFO:: Command: (seqnum-from-serial-number 148 "B" 50)
INFO:: Command: (seqnum-from-serial-number 148 "B" 51)
INFO:: Command: (seqnum-from-serial-number 148 "B" 52)
INFO:: Command: (seqnum-from-serial-number 148 "B" 53)
INFO:: Command: (seqnum-from-serial-number 148 "B" 54)
INFO:: Command: (seqnum-from-serial-number 148 "B" 55)
INFO:: Command: (seqnum-from-serial-number 148 "B" 56)
INFO:: Command: (seqnum-from-serial-number 148 "B" 57)
INFO:: Command: (seqnum-from-serial-number 148 "B" 58)
INFO:: Command: (seqnum-from-serial-number 148 "B" 59)
INFO:: Command: (seqnum-from-serial-number 148 "B" 60)
INFO:: Command: (seqnum-from-serial-number 148 "B" 61)
INFO:: Command: (seqnum-from-serial-number 148 "B" 62)
INFO:: Command: (seqnum-from-serial-number 148 "B" 63)
INFO:: Command: (seqnum-from-serial-number 148 "B" 64)
INFO:: Command: (seqnum-from-serial-number 148 "B" 65)
INFO:: Command: (seqnum-from-serial-number 148 "B" 66)
INFO:: Command: (seqnum-from-serial-number 148 "B" 67)
INFO:: Command: (seqnum-from-serial-number 148 "B" 68)
INFO:: Command: (seqnum-from-serial-number 148 "B" 69)
INFO:: Command: (seqnum-from-serial-number 148 "B" 70)
INFO:: Command: (seqnum-from-serial-number 148 "B" 71)
INFO:: Command: (seqnum-from-serial-number 148 "B" 72)
INFO:: Command: (seqnum-from-serial-number 148 "B" 73)
INFO:: Command: (seqnum-from-serial-number 148 "B" 74)
INFO:: Command: (seqnum-from-serial-number 148 "B" 75)
INFO:: Command: (seqnum-from-serial-number 148 "B" 76)
INFO:: Command: (seqnum-from-serial-number 148 "B" 77)
INFO:: Command: (seqnum-from-serial-number 148 "B" 78)
INFO:: Command: (seqnum-from-serial-number 148 "B" 79)
INFO:: Command: (seqnum-from-serial-number 148 "B" 80)
INFO:: Command: (seqnum-from-serial-number 148 "B" 81)
INFO:: Command: (seqnum-from-serial-number 148 "B" 82)
INFO:: Command: (seqnum-from-serial-number 148 "B" 83)
INFO:: Command: (seqnum-from-serial-number 148 "B" 84)
INFO:: Command: (seqnum-from-serial-number 148 "B" 85)
INFO:: Command: (seqnum-from-serial-number 148 "B" 86)
INFO:: Command: (seqnum-from-serial-number 148 "B" 87)
INFO:: Command: (seqnum-from-serial-number 148 "B" 88)
INFO:: Command: (seqnum-from-serial-number 148 "B" 89)
INFO:: Command: (seqnum-from-serial-number 148 "B" 90)
INFO:: Command: (seqnum-from-serial-number 148 "B" 91)
INFO:: Command: (seqnum-from-serial-number 148 "B" 92)
INFO:: Command: (seqnum-from-serial-number 148 "B" 93)
INFO:: Command: (seqnum-from-serial-number 148 "B" 94)
INFO:: Command: (seqnum-from-serial-number 148 "B" 95)
INFO:: mutate 2 A to a TRP
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_tutorial-modern.pdb_Wed_Aug__2_00:53:39_2017_modification_4.pdb.gz
INFO:: Command: (mutate 148 "A" 2 "" "TRP")
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 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_Wed_Aug__2_00:53:39_2017_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
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 149 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_Wed_Aug__2_00:53:46_2017_modification_0.pdb.gz
INFO:: Command: (mutate 149 "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 149 "B")
DEBUG ncs_control_change_ncs_master_to_chain_update_widget imol: 149 and ichain: 0
DEBUG:: ncs_control_change_ncs_master_to_chain imol: 149 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_Wed_Aug__2_00:53:46_2017_modification_1.pdb.gz
INFO:: backup file coot-backup/_lmb_home_pemsley_data_greg-data_pdb1t6q.ent_Wed_Aug__2_00:53:46_2017_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
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 150 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 150 and chain_id: B
   %%%%%% add_ncs_ghosts_using_ncs_master 
   %%%%%% imaster: 1
   Checking chains for NCS matching to chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first  selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 540 in second selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.4989
    rms devi: 2.7962
    max devi: 6.6860
    min devi: 0.4401
   find_ncs_matrix returns (LSQ) 
|    0.7026,    0.1278,       0.7|
|    0.6024,    0.4169,   -0.6807|
|   -0.3788,    0.8999,    0.2159|
(     62.25,    -87.53,    -9.128)
   Adding ghost with name: NCS found from matching Chain A onto Chain B
INFO:: NCS chain comparison 62/62
First atom of 506 in first  selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 535 in second selection 1/C/190 {GLN}/ N   altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.6728
    rms devi: 2.9369
    max devi: 6.1200
    min devi: 0.2483
   find_ncs_matrix returns (LSQ) 
|   -0.3504,   -0.8022,   -0.4834|
|   -0.7587,  -0.05952,    0.6488|
|   -0.5492,     0.594,   -0.5878|
(    -29.05,     14.61,    -72.53)
   Adding ghost with name: NCS found from matching Chain C onto Chain B
INFO:: NCS chain comparison 61/62
First atom of 506 in first  selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
First atom of 497 in second selection 1/D/193 {SER}/ N   altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had: 
   mean devi: 1.7317
    rms devi: 1.9769
    max devi: 7.9453
    min devi: 0.5297
   find_ncs_matrix returns (LSQ) 
|   -0.3815,   -0.9208,  -0.08098|
|   -0.9191,    0.3685,    0.1396|
|  -0.09874,    0.1277,   -0.9869|
(    -11.18,     4.757,    -127.2)
   Adding ghost with name: NCS found from matching Chain D onto Chain B
INFO:: NCS chain comparison 0/62
INFO:: set_ncs_master_chain Constructed 3 ghosts
   Ghost info:: NCS found from matching Chain A onto Chain B
   Ghost info:: NCS found from matching Chain C onto Chain B
   Ghost info:: NCS found from matching Chain D onto Chain B
INFO:: Command: (copy-molecule 150)
INFO:: Matching/moving molecule number 151 to 150
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_Wed_Aug__2_00:54:02_2017_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 151 to 150
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_Wed_Aug__2_00:54:02_2017_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 151 to 150
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_Wed_Aug__2_00:54:02_2017_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 151)
   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 50)
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 64)
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 76)
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 92)
INFO:: Command: (molecule-name 93)
INFO:: Command: (molecule-name 94)
INFO:: Command: (molecule-name 98)
INFO:: Command: (molecule-name 99)
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 115)
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 133)
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 141)
INFO:: Command: (close-molecule 143)
INFO:: Command: (close-molecule 145)
INFO:: Command: (molecule-name 147)
INFO:: Command: (molecule-name 148)
INFO:: Command: (molecule-name 149)
INFO:: Command: (molecule-name 150)
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
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 152 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:: 0.0320 seconds to read MTZ file
INFO:: 0.0190 seconds to initialize map
INFO:: 0.0210 seconds for FFT
INFO:: Map statistics: mean: -0.0000 st.d: 0.2241
INFO:: Map statistics:  min: -0.8818   max: 1.7219
INFO:: 0.0050 seconds for statistics
      Map mean: ........ -0.0000
      Map sigma: ....... 0.2241
      Map maximum: ..... 1.7219
      Map minimum: ..... -0.8818
INFO:: 0.0230 seconds for contour map
INFO:: 0.1000 seconds in total
INFO:: NCS chain comparison 62/67
First atom of 540 in first  selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 506 in second selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.5700,-74.7200,-82.8480) B-factor: 88.5200
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.4989
    rms devi: 2.7962
    max devi: 6.6860
    min devi: 0.4401
   find_ncs_matrix returns (LSQ) 
|    0.7026,    0.6024,   -0.3788|
|    0.1278,    0.4169,    0.8999|
|       0.7,   -0.6807,    0.2159|
(     5.528,     36.75,    -101.2)
INFO:: NCS chain comparison 66/67
First atom of 540 in first  selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 535 in second selection 1/C/190 {GLN}/ N   altLoc :: segid :: pos: (63.7260,-15.7090,-72.8850) B-factor: 50.7600
INFO:: LSQ matched 66 atoms
INFO:: 66 matched atoms had: 
   mean devi: 1.9713
    rms devi: 2.1729
    max devi: 4.5411
    min devi: 0.4295
   find_ncs_matrix returns (LSQ) 
|   -0.4445,   -0.8903,  -0.09887|
|    -0.893,    0.4317,    0.1271|
|  -0.07049,    0.1448,   -0.9869|
(    -8.624,     7.402,    -127.7)
INFO:: NCS chain comparison 61/67
First atom of 540 in first  selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.5350,-64.4380,-56.9280) B-factor: 45.2600
First atom of 497 in second selection 1/D/193 {SER}/ N   altLoc :: segid :: pos: (62.9170,-35.9890,-55.9290) B-factor: 78.3500
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had: 
   mean devi: 3.7042
    rms devi: 4.0859
    max devi: 9.4383
    min devi: 0.2858
   find_ncs_matrix returns (LSQ) 
|   -0.7198,   -0.6079,    0.3353|
|   -0.5986,    0.2989,   -0.7432|
|    0.3516,   -0.7356,    -0.579|
(     36.14,     -61.4,    -149.3)
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 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)
INFO:: Map statistics: mean: -0.0008 st.d: 0.1767
INFO:: Map statistics:  min: -0.9977   max: 1.4866
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    5946
    0.3997    3628
    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 153 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 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)
INFO:: Map statistics: mean: -0.0008 st.d: 0.1767
INFO:: Map statistics:  min: -0.9977   max: 1.4866
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    5946
    0.3997    3628
    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 153 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 153 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)
INFO:: Map statistics: mean: -0.0008 st.d: 0.1767
INFO:: Map statistics:  min: -0.9977   max: 1.4866
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    5946
    0.3997    3628
    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 50)
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 64)
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 76)
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 92)
INFO:: Command: (molecule-name 93)
INFO:: Command: (molecule-name 94)
INFO:: Command: (molecule-name 98)
INFO:: Command: (molecule-name 99)
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 115)
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 133)
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 141)
INFO:: Command: (molecule-name 147)
INFO:: Command: (molecule-name 148)
INFO:: Command: (molecule-name 149)
INFO:: Command: (molecule-name 150)
INFO:: Command: (molecule-name 152)
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/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_78', '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/rnasa-1.8-all_refmac1.mtz FWT PHWT', '/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 142 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 153 NCS found from matching Chain B onto Chain A', 'Map 153 NCS found from matching Chain C onto Chain A', 'Map 153 NCS found from matching Chain D onto Chain A', 'Map 153 NCS average of Chain A type molecules', 'Map 153 NCS found from matching Chain B onto Chain A', 'Map 153 NCS found from matching Chain C onto Chain A', 'Map 153 NCS found from matching Chain D onto Chain A', 'Map 153 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...
 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] 14.7762
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -54.9516
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 162.6106
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] 8.4938
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -195.4683
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -166.4554
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 0 chiral vol restraints 
created 105 restraints

INFO:: make_restraints(): made 377 non-bonded restraints
initial distortion_score: 24.1438
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.0314
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 332) at 10.8808
    Final Estimated RMS Z Scores:
bonds:      0.0855
angles:     0.3991
torsions:   N/A 
planes:     0.0184
non-bonded: 0.0002
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
ligand eigen values: 36.4975  76.1647  445.5317  
 ligand eigen vectors: 
|  -0.07977,    0.2304,   -0.9698|
|   -0.4027,    0.8825,    0.2428|
|    0.9119,    0.4099,   0.02239|
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] 37.0743
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -49.1207
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 187.9187
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] -11.1421
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -178.1636
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -169.0043
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 0 chiral vol restraints 
created 105 restraints

INFO:: make_restraints(): made 380 non-bonded restraints
initial distortion_score: 165.2660
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.4025
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 359) at 11.0005
    Final Estimated RMS Z Scores:
bonds:      0.0834
angles:     0.4015
torsions:   N/A 
planes:     0.0301
non-bonded: 0.0003
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
ligand eigen values: 40.4491  75.2040  439.3141  
 ligand eigen vectors: 
|  -0.01617,    0.2434,   -0.9698|
|   -0.3291,    0.9146,     0.235|
|    0.9442,     0.323,   0.06531|
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] 12.1869
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -89.8476
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 152.9450
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] -10.1671
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -220.6830
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -138.9559
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 0 chiral vol restraints 
created 105 restraints

INFO:: make_restraints(): made 381 non-bonded restraints
initial distortion_score: 22.6852
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.0273
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 317) at 10.8449
    Final Estimated RMS Z Scores:
bonds:      0.0842
angles:     0.3986
torsions:   N/A 
planes:     0.0357
non-bonded: 0.0002
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
ligand eigen values: 24.7987  97.9331  424.9583  
 ligand eigen vectors: 
|   -0.1827,    0.1536,   -0.9711|
|   -0.2572,    0.9459,     0.198|
|    0.9489,    0.2859,   -0.1333|
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] 22.9319
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -81.4598
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 191.6705
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] -28.0568
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -170.5559
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -164.7228
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 0 chiral vol restraints 
created 105 restraints

INFO:: make_restraints(): made 379 non-bonded restraints
initial distortion_score: 88.7771
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.2018
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 499) at 11.0813
    Final Estimated RMS Z Scores:
bonds:      0.0850
angles:     0.4029
torsions:   N/A 
planes:     0.0042
non-bonded: 0.0002
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
ligand eigen values: 23.5873  88.9388  439.7719  
 ligand eigen vectors: 
|  -0.09012,    0.2069,   -0.9742|
|   -0.1806,    0.9586,    0.2203|
|    0.9794,    0.1958,  -0.04902|
   non-const-non-ring-tors: 0 [torsion-restraint: var_1  N3   C2   N2  HN21 0.0000 20.0000 1] 1.5000
   non-const-non-ring-tors: 1 [torsion-restraint: var_2  C8   N9   C1*  C2* -78.3750 20.0000 1] -90.1820
   non-const-non-ring-tors: 2 [torsion-restraint: var_6  O4*  C4*  C5*  O5* -61.6860 20.0000 3] 167.9219
   non-const-non-ring-tors: 3 [torsion-restraint: var_7  C4*  C5*  O5* HO5* 0.0000 20.0000 1] -20.0368
   non-const-non-ring-tors: 4 [torsion-restraint: var_12  C2*  C3*  O3*  P   -179.7030 20.0000 1] -171.9200
   non-const-non-ring-tors: 5 [torsion-restraint: var_13  C3*  O3*  P    O2P -156.9910 20.0000 1] -156.0362
created 38 bond       restraints 
created 66 angle      restraints 
created 1 plane      restraints 
created 0 chiral vol restraints 
created 105 restraints

INFO:: make_restraints(): made 378 non-bonded restraints
initial distortion_score: 36.6299
    Initial RMS Z values
bonds:      0.1236
angles:     0.4213
torsions:   N/A 
planes:     0.0586
non-bonded: 0.0644
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
Minimum found (iteration number 527) at 11.1991
    Final Estimated RMS Z Scores:
bonds:      0.0845
angles:     0.4053
torsions:   N/A 
planes:     0.0102
non-bonded: 0.0002
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
GemanMcCl:  N/A 
INFO:: Protein centre at: xyz = (     41.53,     8.726,     12.87)
There are 1 clusters
Here are the top 10 clusters:
  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 0.2766
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 125 tests in 276.260s

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
test62_0 (__main__.PdbMtzTestFunctions)
Fix for Oliver Clarke fit by atom selection bug ... 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
test11_0 (__main__.LigandTestFunctions)
pyrogen dictionary does not make double-quoted atom names ... 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 125 tests in 276.260s

OK


Unitest skip does not exist!
The following tests were skipped and marked as passed:
    Libcif horne
    Make a glycosidic linkage
    Pyrogen Runs OK?
    pyrogen dictionary does not make double-quoted atom names


INFO:: Command: (close-molecule 0)
INFO:: Command: (close-molecule 1)
INFO:: Command: (close-molecule 2)
INFO:: Command: (close-molecule 3)
INFO:: Command: (close-molecule 4)
INFO:: Command: (close-molecule 5)
INFO:: Command: (close-molecule 6)
INFO:: Command: (close-molecule 7)
INFO:: Command: (close-molecule 8)
INFO:: Command: (close-molecule 9)
INFO:: Command: (close-molecule 10)
INFO:: Command: (close-molecule 11)
INFO:: Command: (close-molecule 13)
INFO:: Command: (close-molecule 14)
INFO:: Command: (close-molecule 15)
INFO:: Command: (close-molecule 16)
INFO:: Command: (close-molecule 17)
INFO:: Command: (close-molecule 18)
INFO:: Command: (close-molecule 21)
INFO:: Command: (close-molecule 22)
INFO:: Command: (close-molecule 23)
INFO:: Command: (close-molecule 24)
INFO:: Command: (close-molecule 25)
INFO:: Command: (close-molecule 26)
INFO:: Command: (close-molecule 27)
INFO:: Command: (close-molecule 28)
INFO:: Command: (close-molecule 29)
INFO:: Command: (close-molecule 30)
INFO:: Command: (close-molecule 31)
INFO:: Command: (close-molecule 32)
INFO:: Command: (close-molecule 33)
INFO:: Command: (close-molecule 34)
INFO:: Command: (close-molecule 35)
INFO:: Command: (close-molecule 36)
INFO:: Command: (close-molecule 37)
INFO:: Command: (close-molecule 38)
INFO:: Command: (close-molecule 39)
INFO:: Command: (close-molecule 40)
INFO:: Command: (close-molecule 41)
INFO:: Command: (close-molecule 44)
INFO:: Command: (close-molecule 45)
INFO:: Command: (close-molecule 46)
INFO:: Command: (close-molecule 47)
INFO:: Command: (close-molecule 48)
INFO:: Command: (close-molecule 49)
INFO:: Command: (close-molecule 50)
INFO:: Command: (close-molecule 51)
INFO:: Command: (close-molecule 52)
INFO:: Command: (close-molecule 53)
INFO:: Command: (close-molecule 54)
INFO:: Command: (close-molecule 55)
INFO:: Command: (close-molecule 56)
INFO:: Command: (close-molecule 57)
INFO:: Command: (close-molecule 58)
INFO:: Command: (close-molecule 59)
INFO:: Command: (close-molecule 60)
INFO:: Command: (close-molecule 61)
INFO:: Command: (close-molecule 62)
INFO:: Command: (close-molecule 63)
INFO:: Command: (close-molecule 64)
INFO:: Command: (close-molecule 65)
INFO:: Command: (close-molecule 66)
INFO:: Command: (close-molecule 67)
INFO:: Command: (close-molecule 68)
INFO:: Command: (close-molecule 69)
INFO:: Command: (close-molecule 70)
INFO:: Command: (close-molecule 71)
INFO:: Command: (close-molecule 72)
INFO:: Command: (close-molecule 73)
INFO:: Command: (close-molecule 74)
INFO:: Command: (close-molecule 75)
INFO:: Command: (close-molecule 76)
INFO:: Command: (close-molecule 77)
INFO:: Command: (close-molecule 78)
INFO:: Command: (close-molecule 79)
INFO:: Command: (close-molecule 80)
INFO:: Command: (close-molecule 81)
INFO:: Command: (close-molecule 82)
INFO:: Command: (close-molecule 83)
INFO:: Command: (close-molecule 84)
INFO:: Command: (close-molecule 85)
INFO:: Command: (close-molecule 86)
INFO:: Command: (close-molecule 87)
INFO:: Command: (close-molecule 88)
INFO:: Command: (close-molecule 89)
INFO:: Command: (close-molecule 90)
INFO:: Command: (close-molecule 91)
INFO:: Command: (close-molecule 92)
INFO:: Command: (close-molecule 93)
INFO:: Command: (close-molecule 94)
INFO:: Command: (close-molecule 97)
INFO:: Command: (close-molecule 98)
INFO:: Command: (close-molecule 99)
INFO:: Command: (close-molecule 101)
INFO:: Command: (close-molecule 102)
INFO:: Command: (close-molecule 103)
INFO:: Command: (close-molecule 104)
INFO:: Command: (close-molecule 105)
INFO:: Command: (close-molecule 106)
INFO:: Command: (close-molecule 107)
INFO:: Command: (close-molecule 108)
INFO:: Command: (close-molecule 109)
INFO:: Command: (close-molecule 110)
INFO:: Command: (close-molecule 111)
INFO:: Command: (close-molecule 112)
INFO:: Command: (close-molecule 113)
INFO:: Command: (close-molecule 114)
INFO:: Command: (close-molecule 115)
INFO:: Command: (close-molecule 116)
INFO:: Command: (close-molecule 117)
INFO:: Command: (close-molecule 118)
INFO:: Command: (close-molecule 119)
INFO:: Command: (close-molecule 120)
INFO:: Command: (close-molecule 121)
INFO:: Command: (close-molecule 122)
INFO:: Command: (close-molecule 123)
INFO:: Command: (close-molecule 124)
INFO:: Command: (close-molecule 125)
INFO:: Command: (close-molecule 126)
INFO:: Command: (close-molecule 127)
INFO:: Command: (close-molecule 128)
INFO:: Command: (close-molecule 129)
INFO:: Command: (close-molecule 130)
INFO:: Command: (close-molecule 131)
INFO:: Command: (close-molecule 132)
INFO:: Command: (close-molecule 133)
INFO:: Command: (close-molecule 134)
INFO:: Command: (close-molecule 135)
INFO:: Command: (close-molecule 136)
INFO:: Command: (close-molecule 137)
INFO:: Command: (close-molecule 138)
INFO:: Command: (close-molecule 139)
INFO:: Command: (close-molecule 140)
INFO:: Command: (close-molecule 141)
INFO:: Command: (close-molecule 142)
INFO:: Command: (close-molecule 144)
INFO:: Command: (close-molecule 146)
INFO:: Command: (close-molecule 147)
INFO:: Command: (close-molecule 148)
INFO:: Command: (close-molecule 149)
INFO:: Command: (close-molecule 150)
INFO:: Command: (close-molecule 152)
INFO:: Command: (close-molecule 153)
INFO:: Command: (close-molecule 154)
INFO:: Command: (close-molecule 155)
INFO:: Command: (close-molecule 156)
INFO:: Command: (close-molecule 157)
INFO:: Command: (close-molecule 158)
INFO:: Command: (close-molecule 159)
INFO:: Command: (close-molecule 160)
INFO:: Command: (close-molecule 161)
gc: collectable <cell 0x2ac40a1ce830>
gc: collectable <cell 0x2ac40a1bdc58>
gc: collectable <cell 0x2ac4078335c8>
gc: collectable <function 0x2ac40786e500>
gc: collectable <tuple 0x2ac4078618c0>
gc: collectable <function 0x2ac40786e488>

FINALLY collect some GARBAGE

BL INFO:: no of collected carbage items 6

BL DEBUG:: list of garbage items:

     <cell at 0x2ac40a1ce830: function object at 0x2ac40786e488>
     <cell at 0x2ac40a1bdc58: function object at 0x2ac40786e500>
     <cell at 0x2ac4078335c8: module object at 0x2ac407404130>
     <function skip_to_chain_internal at 0x2ac40786e500>
     (<cell at 0x2ac40a1ce830: function object at 0x2ac40786e488>, <cell at 0x2ac40a1bdc58: function object at 0x2ac40786e500>, <cell at 0x2ac4078335c8: module object at 0x2ac407404130>)
     <function skip_to_chain at 0x2ac40786e488>

Detailed information for functions:

  BL INFO:: garbage item and location:
    <function skip_to_chain_internal at 0x2ac40786e500>
    <code object skip_to_chain_internal at 0x2ac407d76130, file "/lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-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 0x2ac40786e488>
    <code object skip_to_chain at 0x2ac407d761b0, file "/lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-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 0.8.9-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