testing with greg
testing with greg
currently we are here:
/home/emsley/autobuild/building/garib-pc-1.lmb.internal_2013-09-13__T03_40_01/coot-0.8-pre
Fri Sep 13 04:44:04 BST 2013
WARNING:: ccp4 setup file setup-ccp4 does not exist.
/home/emsley/autobuild/installed-pre-release-gtk2-python/bin/coot-real --no-graphics --script command-line-greg.scm
INFO:: splash_screen_pixmap_dir /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/pixmaps
INFO:: Colours file: /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/colours.def loaded
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/
There are 125 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif
There are 1 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif
Reading coordinate file: /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/standard-residues.pdb
 PDB file /home/emsley/autobuild/installed-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)
DEBUG:: stating pydirectory /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/python
INFO:: importing coot.py from /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/python/coot.py
Importing python module coot using command from coot import *
INFO:: coot.py imported
INFO loading coot python modules
Running python script /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/python/coot_load_modules.py
Loading: coot_utils.py
load redefine_functions.py
Loading: filter.py
Loading: coot_lsq.py
Loading: shelx.py
Loading: get_ebi.py
Loading: local_code.py
Loading: hello.py
Good Morning None, Welcome to Coot. 0.8-pre (revision 4759)  [with guile 1.8.8 embedded] [with python 2.7.5 embedded]
(set-display-intro-string "Good Morning None, Welcome to Coot. 0.8-pre (revision 4759)  [with guile 1.8.8 embedded] [with python 2.7.5 embedded]")
Loading: mutate.py
Loading: refmac.py
Loading: libcheck.py
Loading: gap.py
Loading: fitting.py
Loading: raster3d.py
Loading: povray.py
Loading: remote_control.py
Loading: generic_objects.py
Loading: ncs.py
Loading: parse_pisa_xml.py
Loading: cns2coot.py
Loading: tips.py
Loading: prodrg_import.py
Loading: jligand.py
Loading: americanisms.py
Loading: group_settings.py
Loading: brute_lsqman.py
INFO:: loading preferences file /home/emsley/.coot-preferences/coot_preferences.py
Running python script /home/emsley/.coot-preferences/coot_preferences.py
(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 13.00)
(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)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
Loading scheme files from /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/scheme
(set-display-intro-string "Good morning Paul. Welcome to Coot")
(set-display-lists-for-maps 0)
INFO:: loading preferences file /home/emsley/.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 13.00)
(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)
INFO:: loading preferences file /home/emsley/.coot-preferences/mogul-interface.scm 
INFO:: loading preferences file /home/emsley/.coot-preferences/test-fit-step.scm 
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
Loading ~/.coot...done.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 0 read successfully
DEBUG:: there were 0 types with no dictionary 
Molecule number -5 is not a valid model molecule
Reading coordinate file: /home/emsley/data/greg-data/2WF6.cif
 mmCIF file /home/emsley/data/greg-data/2WF6.cif has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 1 read successfully
DEBUG:: there were 3 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "ALF"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALF.cif
INFO:: using standard CCP4 Refmac dictionary to search for "MG"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MG.cif
INFO:: using standard CCP4 Refmac dictionary to search for "BG6"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/b/BG6.cif
in new_molecule_by_atom_selection Something bad happened - No atoms selected
Reading coordinate file: /home/emsley/data/greg-data/ins-code-fragment-pre.pdb
 PDB file /home/emsley/data/greg-data/ins-code-fragment-pre.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 2 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Creating directory coot-backup
INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:44:04_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:44:04_2013_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_ins-code-fragment-pre.pdb_Fri_Sep_13_04:44:04_2013_modification_2.pdb.gz
WARNING:: Error reading bogus.map
Read map bogus.map failed
WARNING:: Can't find file bogus.mtz
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.035 seconds to initialize map
INFO:: 0.034 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.05 seconds for contour map
INFO:: 0.152 seconds in total
WARNING:: file xx-missing.mtz does not exist
>>>>>> CCP4 library signal library_file:End of File (Error)
	 raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 0:Success (Error)
	 raised in ccp4_file_rarch <<<<<<
>>>>>> CCP4 library signal library_file:End of File (Error)
	 raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 0:Success (Error)
	 raised in ccp4_file_readint <<<<<<
>>>>>> System signal 0:Success (Error)
	 raised in ccp4_file_read <<<<<<
>>>>>> CCP4 library signal library_file:End of File (Error)
	 raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 0:Success (Error)
	 raised in ccp4_file_readchar <<<<<<
>>>>>> CCP4 library signal mtz:Read failed (Error)
	 raised in MtzGet <<<<<<
CCP4MTZfile: open_read - File missing or corrupted: /home/emsley/data/greg-data/broken.mtz
INFO:: not an mtz file: /home/emsley/data/greg-data/broken.mtz
making conventional map from MTZ filename /home/emsley/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:: 0.024 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.034 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.047 seconds for contour map
INFO:: 0.109 seconds in total
valid_labels(/home/emsley/data/greg-data/3hfl_sigmaa.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/data/greg-data/3hfl_sigmaa.mtz
Number of OBSERVED reflections: 17920
INFO:: finding ASU unique map points with sampling rate 2.2
INFO grid sampling...Nuvw = (  96, 128, 132)
INFO:: 0.022 seconds to read MTZ file
INFO:: 0.018 seconds to initialize map
INFO:: 0.029 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.83254e-11
      Map sigma: ....... 0.260405
      Map maximum: ..... 1.77531
      Map minimum: ..... -1.05473
INFO:: 0.011 seconds for contour map
INFO:: 0.083 seconds in total
INFO:: map file type was determined to be CCP4 type
allocating space in read_ccp4_map
attempting to read CCP4 map: test-3hfl.map
========== file grid sampling: Nuvw = (  96, 128, 132)
closing CCP4 map: test-3hfl.map
Map statistics: mean: 1.83254e-11 st.d: 0.260405
Map statistics: min: -1.05473, max: 1.77531
-0.983981    17
-0.842479    308
-0.700977    2677
-0.559475    12833
-0.417973    39023
-0.276471    86235
-0.134969    183659
0.00653285    251917
0.148035    122819
0.289537    40550
0.431039    26756
0.572541    19978
0.714043    13210
0.855545    6970
0.997047    2820
 1.13855    873
 1.28005    243
 1.42155    85
 1.56306    25
 1.70456    10
 1.84606    0
      Map mean: ........ 1.83254e-11
      Map rmsd: ........ 0.260405
      Map maximum: ..... 1.77531
      Map minimum: ..... -1.05473
Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb
 PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 83/90
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 7 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Masking around 41 atoms
fitting terminal residue with 100 random trials
INFO:: Fitting terminal residue  without individual rigid body fitting.
 A 0 ALA  N   :: xyz = (     49.89,     13.56,     4.156)
 A 0 ALA  C   :: xyz = (     49.65,     11.73,     2.525)
 A 0 ALA  CA  :: xyz = (     49.26,     12.27,     3.898)
 A 0 ALA  O   :: xyz = (     49.63,     10.53,     2.245)
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:05_2013_modification_0.pdb.gz
Symmetry available for this molecule
INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:05_2013_modification_0.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb
 PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 9 read successfully
DEBUG:: there were 0 types with no dictionary 
DEUBG:: add_terminal_residue_using_phi_psi() 275
INFO:: backup file coot-backup/_home_emsley_data_greg-data_frag-2wot.pdb_Fri_Sep_13_04:44:05_2013_modification_0.pdb.gz
adding whole residue triggered by atom 1/A/276 {ALA}/ N   altLoc :: segid :: pos: (7.95956,25.0769,3.88408) B-factor: 30  with element  N
adding atom to existing residue 1/A/276 {ALA}/ C   altLoc :: segid :: pos: (10.3577,25.1553,4.43381) B-factor: 30 (already has 1 atoms)
adding atom to existing residue 1/A/276 {ALA}/ CA  altLoc :: segid :: pos: (9.26201,24.4785,3.6171) B-factor: 30 (already has 2 atoms)
adding atom to existing residue 1/A/276 {ALA}/ O   altLoc :: segid :: pos: (10.6535,24.7432,5.55546) B-factor: 30 (already has 3 atoms)
adding atom to existing residue 1/A/276 {ALA}/ CB  altLoc :: segid :: pos: (9.55539,24.5518,2.12418) B-factor: 30 (already has 4 atoms)
INFO:: 4 atoms added to molecule.
INFO:: old n_atoms: 76 new: 81
DEUBG:: add_terminal_residue_using_phi_psi() 276
INFO:: backup file coot-backup/_home_emsley_data_greg-data_frag-2wot.pdb_Fri_Sep_13_04:44:05_2013_modification_1.pdb.gz
adding whole residue triggered by atom 1/A/277 {ALA}/ N   altLoc :: segid :: pos: (10.5277,26.4564,4.22323) B-factor: 30  with element  N
adding atom to existing residue 1/A/277 {ALA}/ C   altLoc :: segid :: pos: (11.3064,27.175,6.44508) B-factor: 30 (already has 1 atoms)
adding atom to existing residue 1/A/277 {ALA}/ CA  altLoc :: segid :: pos: (11.5409,27.2225,4.93896) B-factor: 30 (already has 2 atoms)
adding atom to existing residue 1/A/277 {ALA}/ O   altLoc :: segid :: pos: (11.8153,26.2914,7.13472) B-factor: 30 (already has 3 atoms)
adding atom to existing residue 1/A/277 {ALA}/ CB  altLoc :: segid :: pos: (11.5498,28.6554,4.42226) B-factor: 30 (already has 4 atoms)
INFO:: 4 atoms added to molecule.
INFO:: old n_atoms: 81 new: 86
DEUBG:: add_terminal_residue_using_phi_psi() 276
WARNING:: add_terminal_residue_using_phi_psi() residue not found for "XX" 276
Symmetry available for this molecule
Symmetry available for this molecule
 N  /10/B is not found in this molecule: (11) atom selection from tutorial-modern.pdb
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:05_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:05_2013_modification_1.pdb.gz
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:05_2013_modification_2.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/rotamer-test-fragment.pdb
 PDB file /home/emsley/data/greg-data/rotamer-test-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 12 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 ""]
Reading coordinate file: /home/emsley/data/greg-data/res098.pdb
 PDB file /home/emsley/data/greg-data/res098.pdb has been read.
Spacegroup: P 41 21 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 13 read successfully
DEBUG:: there were 0 types with no dictionary 
created 6 bond       restraints 
created 6 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 13 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 15 and 15 of chain X
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
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
initial distortion_score: 9.10451
    Initial RMS Z values
bonds:      0.404934
angles:     0.452855
torsions:   N/A 
planes:     1.15167
non-bonded: 0
chiral vol: 0.162676
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 186) at 6.27245
    Final Estimated RMS Z Scores:
bonds:      0.0592078
angles:     0.539637
torsions:   N/A 
planes:     0.807452
non-bonded: 0
chiral vol: 0.376827
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 2.221
debug:: restraints results 1 5 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_res098.pdb_Fri_Sep_13_04:44:06_2013_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 14 read successfully
DEBUG:: there were 0 types with no dictionary 
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.025 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.033 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.05 seconds for contour map
INFO:: 0.111 seconds in total
here in split_residue() 
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:07_2013_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0 
debug:: split_residue() returned 0 ""
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:07_2013_modification_1.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 12.0506
Reading coordinate file: /home/emsley/data/greg-data/pdb3knw.ent
 PDB file /home/emsley/data/greg-data/pdb3knw.ent has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 30 links
Symmetry available for this molecule
INFO:: NCS chain comparison 185/199
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 16 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "EDO"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/e/EDO.cif
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3knw.ent_Fri_Sep_13_04:44:07_2013_modification_0.pdb.gz
load "filter.scm"
load "matrices.scm"
load "coot-utils.scm"
load "redefine-functions.scm"
load "json-reader.scm"
load "coot-lsq.scm"
load "shelx.scm"
load "get-ebi.scm"
load "local-code.scm"
load "hello.scm"
Good morning Paul Emsley. Welcome to Coot 0.8-pre (revision 4759)  [with guile 1.8.8 embedded] [with python 2.7.5 embedded].
load "mutate.scm"
load "refmac.scm"
load "brute-lsqman.scm"
load "libcheck.scm"
load "gap.scm"
load "fitting.scm"
load "raster3d.scm"
load "povray.scm"
load "remote-control.scm"
load "generic-objects.scm"
load "fascinating-things.scm"
load "ncs.scm"
load "parse-pisa-xml.scm"
load "cns2coot.scm"
load "clear-backup.scm"
load "tips.scm"
load "prodrg-import.scm"
load "jligand.scm"
load "americanisms.scm"
load "group-settings.scm"

                 === greg-tests tests ===

Loading greg-tests/begin.grg ...
===============================================================
==================== Testing ==================================
===============================================================
Loaded greg-tests/begin.grg
Running 01-pdb+mtz.scm ...
Entered testcase - Post Go To Atom no molecules
PASS: Post Go To Atom no molecules
Entered testcase - Close bad molecule
PASS: Close bad molecule
Entered testcase - Read coordinates test
PASS: Read coordinates test
Entered testcase - New molecule from bogus molecule
PASS: New molecule from bogus molecule
Entered testcase - Don't crash on empty NCS from mmCIF file
   closing molecule number 1
PASS: Don't crash on empty NCS from mmCIF file
Entered testcase - New molecule from bogus atom selection
   INFO:: pre-n-molecules 2   post-n-molecules 2
PASS: New molecule from bogus atom selection
Entered testcase - ins code change and Goto atom over an ins code break
   pre and post ins codes: "" "A"
   pass: ("A" 68 "" " CA ") 
   pass: ("A" 68 "B" " CA ") 
   pass: ("A" 68 "B" " CA ") 
   pass: ("A" 68 "B" " CA ") 
   pass: ("A" 68 "A" " CA ") 
   pass: ("A" 68 "" " CA ") 
   pass: ("A" 66 "" " CA ") 
PASS: ins code change and Goto atom over an ins code break
Entered testcase - Read a bogus map
PASS: Read a bogus map
Entered testcase - Read MTZ test
PASS: Read MTZ test
Entered testcase - Auto-read bad MTZ test
   got status: -1
   got status: -1
PASS: Auto-read bad MTZ test
Entered testcase - Map Sigma 
   INFO:: map sigmas 0.311500996351242 #f
PASS: Map Sigma 
Entered testcase - Another Level Test
PASS: Another Level Test
Entered testcase - Sharpen map from map
PASS: Sharpen map from map
Entered testcase - Set Atom Attribute Test
PASS: Set Atom Attribute Test
Entered testcase - Add Terminal Residue Test
PASS: Add Terminal Residue Test
Entered testcase - Adding residue by phi psi, no crash
PASS: Adding residue by phi psi, no crash
Entered testcase - Select by Sphere
   Sphere mol: there are 4 residues in chain "B"
   Found 20 sphere atoms 
PASS: Select by Sphere
Entered testcase - Test Views
PASS: Test Views
Entered testcase - Label Atoms and Delete
PASS: Label Atoms and Delete
Entered testcase - Rotamer outliers
PASS: Rotamer outliers
Entered testcase - Alt Conf Occ Sum Reset
   For atom " CE " "A" returning occ 0.699999988079071
   For atom " CE " "B" returning occ 0.200000002980232
   For atom " NZ " "A" returning occ 0.699999988079071
   For atom " NZ " "B" returning occ 0.200000002980232
   For atom " CE " "A" returning occ 0.699999988079071
   For atom " CE " "B" returning occ 0.200000002980232
   For atom " NZ " "A" returning occ 0.699999988079071
   For atom " NZ " "B" returning occ 0.200000002980232
   test for closeness: 1.79999998211861 1.79999998211861
PASS: Alt Conf Occ Sum Reset
Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue
PASS: Correct occupancies after auto-fit rotamer on alt-confed residue
Entered testcase - Rotamers work on MSE
    se-1: (("SE  " "") (0.699999988079071 2.0 "SE" "") (58.7999992370605 66.5329971313477 0.0469999983906746))
    se-2: (("SE  " "") (0.699999988079071 2.0 "SE" "") (60.1311187744141 69.3484802246094 -0.673518776893616))
PASS: Rotamers work on MSE
Entered testcase - Splitting residuReading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 17 read successfully
DEBUG:: there were 0 types with no dictionary 
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.024 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.033 seconds for FFT
INFO:: 0.002 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.049 seconds for contour map
INFO:: 0.109 seconds in total
here in split_residue() 
DEBUG:: split_residue table 
   0  N   ::
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:07_2013_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0 
debug:: split_residue() returned 0 ""
Reading coordinate file: /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb
 PDB file /home/emsley/data/greg-data/alt-conf-pepflip-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 19 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-pepflip-test.pdb_Fri_Sep_13_04:44:08_2013_modification_0.pdb.gz
flipped 65 A
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 20 read successfully
DEBUG:: there were 0 types with no dictionary 
in molecule_class_info_t::cis_trans_conversion() atom_sel.mol is 0x3347530
omega: 1 12.7704 degrees 
INFO This is a CIS peptide - making it TRANS
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_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/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_modification_2.pdb.gz
created 10 bond       restraints 
created 10 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 21 restraints

INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A
Link restraints: 
   1 bond    links
   3 angle   links
   2 plane   links
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
initial distortion_score: 3397.26
    Initial RMS Z values
bonds:      15.4679
angles:     7.38705
torsions:   N/A 
planes:     2.80521
non-bonded: 48.7437
chiral vol: 3.04463
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 36) at -4817.07
    Final Estimated RMS Z Scores:
bonds:      2.38716
angles:     1.52188
torsions:   N/A 
planes:     2.38488
non-bonded: 0.638809
chiral vol: 0.226738
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 3.876
Refinement elapsed time: 0.016
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_modification_3.pdb.gz
INFO:: replace_coords: 11 atoms updated.
INFO:: mutate 11 A to a LEU
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_modification_5.pdb.gz
INFO:: replace_coords: 8 atoms updated.
Fitting score for best rotamer: 8.73012
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
   3 angle   links
   2 plane   links
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
initial distortion_score: -5997.66
    Initial RMS Z values
bonds:      1.78865
angles:     1.67802
torsions:   N/A 
planes:     3.14799
non-bonded: 0.634811
chiral vol: 0.191647
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 74) at -6102.11
    Final Estimated RMS Z Scores:
bonds:      2.1245
angles:     1.35379
torsions:   N/A 
planes:     2.43993
non-bonded: 0.278486
chiral vol: 0.408672
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 4.005
Refinement elapsed time: 0.015
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Fri_Sep_13_04:44:08_2013_modification_6.pdb.gz
INFO:: replace_coords: 15 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 21 read successfully
DEBUG:: there were 0 types with no dictionary 
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.024 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.032 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.048 seconds for contour map
INFO:: 0.108 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_link_restraints) returned 1 residues (for link restraints) between (and including) residues 72 and 72 of chain B
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
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
initial distortion_score: -2746.24
    Initial RMS Z values
bonds:      1.67379
angles:     1.06965
torsions:   N/A 
planes:     0.911782
non-bonded: 9.24559
chiral vol: 1.46202
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 13) at -2930.98
    Final Estimated RMS Z Scores:
bonds:      1.17098
angles:     1.38116
torsions:   N/A 
planes:     1.07209
non-bonded: 1.06154
chiral vol: 0.446598
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 4.414
Refinement elapsed time: 0.007
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:09_2013_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb
 PDB file /home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 83/90
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 23 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/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:09_2013_modification_0.pdb.gz
split_residue(int atom_index, int alt_conf_split_type) returns 0 
debug:: split_residue() returned 0 ""
created 20 bond       restraints 
created 23 angle      restraints 
created 0 plane      restraints 
created 4 chiral vol restraints 
created 47 restraints

Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
Flanking residue restraints: 
   5 bond    links
   15 angle   links
   10 plane   links
initial distortion_score: -11033.5
    Initial RMS Z values
bonds:      1.8061
angles:     0.891239
torsions:   N/A 
planes:     1.07498
non-bonded: 0
chiral vol: 0.668982
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 25) at -11238.9
    Final Estimated RMS Z Scores:
bonds:      1.07026
angles:     0.634336
torsions:   N/A 
planes:     0.854652
non-bonded: 0
chiral vol: 0.212403
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 4.974
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:09_2013_modification_1.pdb.gz
INFO:: replace_coords: 23 atoms updated.
created 36 bond       restraints 
created 40 angle      restraints 
created 3 plane      restraints 
created 5 chiral vol restraints 
created 84 restraints

Link restraints: 
   4 bond    links
   12 angle   links
   8 plane   links
Flanking residue restraints: 
   2 bond    links
   6 angle   links
   4 plane   links
initial distortion_score: -13426.3
    Initial RMS Z values
bonds:      0.980695
angles:     1.01754
torsions:   N/A 
planes:     3.84002
non-bonded: 0.677622
chiral vol: 10.2816
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 28) at -16252.4
    Final Estimated RMS Z Scores:
bonds:      1.61921
angles:     1.6368
torsions:   N/A 
planes:     1.89061
non-bonded: 0.00148114
chiral vol: 2.20098
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 5.378
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-add-terminal-1-test.pdb_Fri_Sep_13_04:44:09_2013_modification_2.pdb.gz
INFO:: replace_coords: 41 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 24 read successfully
DEBUG:: there were 0 types with no dictionary 
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.024 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.032 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.048 seconds for contour map
INFO:: 0.108 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
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
initial distortion_score: -9612.98
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     4.28599
non-bonded: 0.734803
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 54) at -11863.7
    Final Estimated RMS Z Scores:
bonds:      1.68281
angles:     1.81047
torsions:   N/A 
planes:     2.09142
non-bonded: 0.00336553
chiral vol: 2.42505
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 5.9
Refinement elapsed time: 0.088
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
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
initial distortion_score: -1426.62
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     4.28599
non-bonded: 0.734803
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 10) at -2820.69
    Final Estimated RMS Z Scores:
bonds:      0.476411
angles:     1.30327
torsions:   N/A 
planes:     1.97227
non-bonded: 0.00079874
chiral vol: 1.28202
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.053
Refinement elapsed time: 0.152
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
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
initial distortion_score: -424.029
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     4.28599
non-bonded: 0.734803
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 2) at -1731.74
    Final Estimated RMS Z Scores:
bonds:      0.349261
angles:     1.23969
torsions:   N/A 
planes:     1.95913
non-bonded: 0.000572745
chiral vol: 1.1417
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.202
Refinement elapsed time: 0.149
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
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
initial distortion_score: 44.0016
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     4.28599
non-bonded: 0.734803
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 63) at -1225.73
    Final Estimated RMS Z Scores:
bonds:      0.298593
angles:     1.21292
torsions:   N/A 
planes:     1.94519
non-bonded: 0.000517479
chiral vol: 1.08218
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.397
Refinement elapsed time: 0.194
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
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
initial distortion_score: 323.047
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     4.28599
non-bonded: 0.734803
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 2) at -924.971
    Final Estimated RMS Z Scores:
bonds:      0.272194
angles:     1.19712
torsions:   N/A 
planes:     1.93037
non-bonded: 0.00050089
chiral vol: 1.04579
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.649
Refinement elapsed time: 0.251
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
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
initial distortion_score: 507.762
    Initial RMS Z values
bonds:      0.935808
angles:     1.05798
torsions:   N/A 
planes:     4.28599
non-bonded: 0.734803
chiral vol: 11.4845
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 27) at -726.414
    Final Estimated RMS Z Scores:
bonds:      0.256858
angles:     1.18565
torsions:   N/A 
planes:     1.91639
non-bonded: 0.000498455
chiral vol: 1.02023
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 6.89
Refinement elapsed time: 0.241
Reading coordinate file: /home/emsley/data/greg-data/alt-conf-waters.pdb
 PDB file /home/emsley/data/greg-data/alt-conf-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 26 read successfully
DEBUG:: there were 0 types with no dictionary 
masking....masking done
INFO:: backup file coot-backup/_home_emsley_data_greg-data_alt-conf-waters.pdb_Fri_Sep_13_04:44:11_2013_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 
Reading coordinate file: /home/emsley/data/greg-data/backrub-fragment.pdb
 PDB file /home/emsley/data/greg-data/backrub-fragment.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 27 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Fri_Sep_13_04:44:12_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_backrub-fragment.pdb_Fri_Sep_13_04:44:12_2013_modification_1.pdb.gz
INFO:: replace_coords: 14 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/coords-B3A.pdb
 PDB file /home/emsley/data/greg-data/coords-B3A.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 29 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "B3A"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/b/B3A.cif
created 5 bond       restraints 
created 5 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 11 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 2.9511
    Initial RMS Z values
bonds:      0.661891
angles:     0.373663
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.249961
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 28) at 4.05831e-05
    Final Estimated RMS Z Scores:
bonds:      0.000532687
angles:     0.00277865
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.00074825
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 7.766
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Fri_Sep_13_04:44:12_2013_modification_0.pdb.gz
INFO:: replace_coords: 6 atoms updated.
WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/lib-B3A.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/lib-B3A.cif had no bond restraints
created 5 bond       restraints 
created 5 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 11 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 4.05831e-05
    Initial RMS Z values
bonds:      0.000532687
angles:     0.00277865
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.00074825
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 2) at 3.06826e-05
    Final Estimated RMS Z Scores:
bonds:      0.00034354
angles:     0.0024396
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.00057811
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 7.835
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Fri_Sep_13_04:44:12_2013_modification_1.pdb.gz
INFO:: replace_coords: 6 atoms updated.
There are 3 data in /home/emsley/data/greg-data/lib-both.cif
Welcome to Coot
created 5 bond       restraints 
created 5 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 11 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 3.01935
    Initial RMS Z values
bonds:      0.670842
angles:     0.375491
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.253458
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 30) at 3.9422e-06
    Final Estimated RMS Z Scores:
bonds:      0.000590566
angles:     0.000608582
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.000588644
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 7.904
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_coords-B3A.pdb_Fri_Sep_13_04:44:12_2013_modification_2.pdb.gz
INFO:: replace_coords: 6 atoms updated.
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,/RNASE3GMP/COMPLEX/FWT,/RNASE3GMP/COMPLEX/PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.025 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.032 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.043 seconds for contour map
INFO:: 0.103 seconds in total
INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible.
Reading coordinate file: /home/emsley/data/greg-data/test-TER-OXT.pdb
 PDB file /home/emsley/data/greg-data/test-TER-OXT.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 31 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_test-TER-OXT.pdb_Fri_Sep_13_04:44:13_2013_modification_0.pdb.gz
Added OXT at 1/A/14 {ASP}/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45
WARNING:: This residue already has an OXT - aborting
Reading coordinate file: /home/emsley/data/greg-data/val.pdb
 PDB file /home/emsley/data/greg-data/val.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 32 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: mutate 3 C to a HIS
INFO:: backup file coot-backup/_home_emsley_data_greg-data_val.pdb_Fri_Sep_13_04:44:13_2013_modification_0.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/2yie-frag.pdb
 PDB file /home/emsley/data/greg-data/2yie-frag.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 33 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_2yie-frag.pdb_Fri_Sep_13_04:44:13_2013_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
Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb
 PDB file /home/emsley/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 34 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "NCO"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NCO.cif
INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Fri_Sep_13_04:44:14_2013_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
Reading coordinate file: /home/emsley/data/greg-data/4f8g.pdb
 PDB file /home/emsley/data/greg-data/4f8g.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 35 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_4f8g.pdb_Fri_Sep_13_04:44:14_2013_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
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.025 seconds to read MTZ file
INFO:: 0 seconds to initialize map
INFO:: 0.033 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.042 seconds for contour map
INFO:: 0.103 seconds in total
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.024 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.032 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.041 seconds for contour map
INFO:: 0.101 seconds in total
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 38 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: Masking around 64 atoms
Map statistics: mean: -0.00140896 st.d: 0.305562
Map statistics: min: -0.921659, max: 3.05176
-0.822323    82
-0.623652    4584
-0.424981    63986
-0.22631    186046
-0.0276392    273649
0.171032    117231
0.369703    35042
0.568374    22373
0.767045    16065
0.965716    9789
 1.16439    5062
 1.36306    2263
 1.56173    811
  1.7604    219
 1.95907    53
 2.15774    10
 2.35641    9
 2.55508    3
 2.75376    2
 2.95243    1
  3.1511    0
e leaves no atoms with negative occupancy
PASS: Splitting residue leaves no atoms with negative occupancy
Entered testcase - Pepflip flips the correct alt confed atoms
PASS: Pepflip flips the correct alt confed atoms
Entered testcase - Correction of CISPEP test
   CISPEPs: "3"
PASS: Correction of CISPEP test
Entered testcase - Refine Zone with Alt conf
   refined moved: d=0.29338761868981
PASS: Refine Zone with Alt conf
Entered testcase - Sphere Refine
======= got bond length 1.29549296880026
PASS: Sphere Refine
Entered testcase - Refinement gives useful results
   refinement results: ("" 0 (("Bonds" "Bonds:    1.683" 1.6828066110611) ("Angles" "Angles:   1.810" 1.81047487258911) ("Planes" "Planes:   2.091" 2.09142184257507) ("Non-bonded" "Non-bonded:   0.058" 0.0580132193863392) ("Chirals" "Chirals:   2.425" 2.4250476360321)))
   ow factor: 2.00243774056435
   INFO:: setting refinement weight to 14.963500637066
   refinement results: ("" 0 (("Bonds" "Bonds:    0.476" 0.476411163806915) ("Angles" "Angles:   1.303" 1.30327272415161) ("Planes" "Planes:   1.972" 1.97226870059967) ("Non-bonded" "Non-bonded:   0.028" 0.028261985629797) ("Chirals" "Chirals:   1.282" 1.28201711177826)))
   ow factor: 1.25849242508411
   INFO:: setting refinement weight to 9.44782857351441
   refinement results: ("" 0 (("Bonds" "Bonds:    0.349" 0.349261254072189) ("Angles" "Angles:   1.240" 1.23969268798828) ("Planes" "Planes:   1.959" 1.95912933349609) ("Non-bonded" "Non-bonded:   0.024" 0.0239320993423462) ("Chirals" "Chirals:   1.142" 1.14170038700104)))
   ow factor: 1.1724459156394
   INFO:: setting refinement weight to 6.87300018487727
   refinement results: ("" 0 (("Bonds" "Bonds:    0.299" 0.29859334230423) ("Angles" "Angles:   1.213" 1.21292293071747) ("Planes" "Planes:   1.945" 1.94519364833832) ("Non-bonded" "Non-bonded:   0.023" 0.0227481555193663) ("Chirals" "Chirals:   1.082" 1.08217918872833)))
   ow factor: 1.13472227752209
   INFO:: setting refinement weight to 5.33786014132015
   refinement results: ("" 0 (("Bonds" "Bonds:    0.272" 0.272194415330887) ("Angles" "Angles:   1.197" 1.19711756706238) ("Planes" "Planes:   1.930" 1.93037307262421) ("Non-bonded" "Non-bonded:   0.022" 0.022380568087101) ("Chirals" "Chirals:   1.046" 1.04578804969788)))
   ow factor: 1.11136827617884
   INFO:: setting refinement weight to 4.32166596876805
   refinement results: ("" 0 (("Bonds" "Bonds:    0.257" 0.256858438253403) ("Angles" "Angles:   1.186" 1.18564605712891) ("Planes" "Planes:   1.916" 1.91639447212219) ("Non-bonded" "Non-bonded:   0.022" 0.0223261024802923) ("Chirals" "Chirals:   1.020" 1.02023339271545)))
   ow factor: 1.09478309005499
PASS: Refinement gives useful results
Entered testcase - Rigid Body Refine Alt Conf Waters
PASS: Rigid Body Refine Alt Conf Waters
Entered testcase - Setting multiple atom attributes
PASS: Setting multiple atom attributes
Entered testcase - Tweak Alt Confs on Active Residue
PASS: Tweak Alt Confs on Active Residue
Entered testcase - Backrub rotamer
PASS: Backrub rotamer
Entered testcase - Libcif horne




PASS: Libcif horne
Entered testcase - Refmac Parameters Storage
PASS: Refmac Parameters Storage
Entered testcase - OXT is added before TER record - add only one
   found TER "TER      25      ASP A  14                                                      "
PASS: OXT is added before TER record - add only one
Entered testcase - The position of the oxygen after a mutation
PASS: The position of the oxygen after a mutation
Entered testcase - TER is at the end of a nucleotide after mutation
PASS: TER is at the end of a nucleotide after mutation
Entered testcase - C7 is removed on mutation from a DC
PASS: C7 is removed on mutation from a DC
Entered testcase - C7 is added on mutation to a DC
DEBUG:: atoms is (" P  " " OP1" " OP2" " O5'" " C5'" " C4'" " O4'" " C3'" " O3'" " C2'" " C1'" " N1 " " C2 " " N3 " " C4 " " C5 " " C6 " " O2 " " O4 " " C7 ")
PASS: C7 is added on mutation to a DC
Entered testcase - Mask and difference map
   high-values: (0.989829301834106 0.952502369880676 1.01570284366608 0.636203646659Map statistics: mean: -0.00140896 st.d: 0.0605043
Map statistics: min: -2.99276, max: 0.774316
-2.89858    4
-2.71023    3
-2.52188    6
-2.33352    5
-2.14517    7
-1.95681    8
-1.76846    18
-1.58011    41
-1.39175    76
 -1.2034    172
-1.01505    335
-0.826691    597
-0.638337    793
-0.449984    1105
-0.26163    1562
-0.0732758    724217
0.115078    4310
0.303432    3125
0.491786    838
 0.68014    58
0.868493    0
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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 seconds to initialize map
INFO:: 0.035 seconds for FFT
INFO:: 0.003 seconds for statistics
      Map mean: ........ 1.22866e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.05176
      Map minimum: ..... -0.921659
INFO:: 0.048 seconds for contour map
INFO:: 0.114 seconds in total
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.025 seconds to read MTZ file
INFO:: 0.048 seconds to initialize map
INFO:: 0.045 seconds for FFT
INFO:: 0.004 seconds for statistics
      Map mean: ........ 1.16132e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 3.07133
      Map minimum: ..... -0.877519
INFO:: 0.054 seconds for contour map
INFO:: 0.176 seconds in total
Map statistics: mean: -3.34695e-06 st.d: 0.311048
Map statistics: min: -0.916532, max: 3.05151
-0.817331    86
-0.618929    5071
-0.420526    68107
-0.222124    192102
-0.0237222    261140
 0.17468    116277
0.373082    35835
0.571484    23249
0.769886    16639
0.968288    10089
 1.16669    5201
 1.36509    2311
 1.56349    835
  1.7619    228
  1.9603    60
  2.1587    18
  2.3571    14
 2.55551    9
 2.75391    6
 2.95231    3
 3.15071    0
Map statistics: mean: 3.34818e-06 st.d: 0.00108591
Map statistics: min: -0.0109202, max: 0.00950789
-0.0104095    5
-0.00938806    12
-0.00836666    25
-0.00734526    37
-0.00632385    61
-0.00530245    326
-0.00428105    1710
-0.00325964    6306
-0.00223824    24803
-0.00121684    106344
-0.000195435    362832
0.000825968    177538
0.00184737    36579
0.00286877    12395
0.00389018    5092
0.00491158    2108
0.00593298    781
0.00695439    243
0.00797579    65
0.00899719    18
0.0100186    0
Reading coordinate file: /home/emsley/data/greg-data/multi-carbo-coot-2.pdb
 PDB file /home/emsley/data/greg-data/multi-carbo-coot-2.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 45 read successfully
DEBUG:: there were 2 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "FUC"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/f/FUC.cif
INFO:: using standard CCP4 Refmac dictionary to search for "NAG"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAG.cif
created 46 bond       restraints 
created 82 angle      restraints 
created 2 plane      restraints 
created 8 chiral vol restraints 
created 138 restraints

INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A
INFO:: glycosidic_linkage type :ALPHA1-4:
Link restraints: 
   1 bond    links
   3 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 7100.08
    Initial RMS Z values
bonds:      11.3589
angles:     3.25886
torsions:   N/A 
planes:     0.0835273
non-bonded: 0.0943839
chiral vol: 0.903463
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 894) at 0.755133
    Final Estimated RMS Z Scores:
bonds:      0.0228192
angles:     0.0911278
torsions:   N/A 
planes:     0.00142033
non-bonded: 5.56479e-06
chiral vol: 0.0465342
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 12.559
debug:: restraints results 1 5 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_multi-carbo-coot-2.pdb_Fri_Sep_13_04:44:17_2013_modification_0.pdb.gz
INFO:: replace_coords: 46 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/monomer-VAL.pdb
 PDB file /home/emsley/data/greg-data/monomer-VAL.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 46 read successfully
DEBUG:: there were 0 types with no dictionary 
created 14 bond       restraints 
created 25 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 40 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
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 
Minimum found (iteration number 80) at 0.247633
    Final Estimated RMS Z Scores:
bonds:      0.0110165
angles:     0.0948618
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.144792
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 13.196
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:17_2013_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
INFO:: undo molecule number set to: 46
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:17_2013_modification_1.pdb.gz
restoring from backup 2 2
Reading coordinate file: coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:17_2013_modification_0.pdb.gz
 PDB file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:17_2013_modification_0.pdb.gz has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2
created 14 bond       restraints 
created 25 angle      restraints 
created 0 plane      restraints 
created 1 chiral vol restraints 
created 40 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
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 
Minimum found (iteration number 80) at 0.247633
    Final Estimated RMS Z Scores:
bonds:      0.0110165
angles:     0.0948618
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.144792
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 13.282
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-VAL.pdb_Fri_Sep_13_04:44:18_2013_modification_0.pdb.gz
INFO:: replace_coords: 15 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb
 PDB file /home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 47 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:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 6 and 6 of chain B
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 1370.91
    Initial RMS Z values
bonds:      5.62114
angles:     3.43297
torsions:   N/A 
planes:     N/A 
non-bonded: 3.49142
chiral vol: 0.753357
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 282) at 0.473499
    Final Estimated RMS Z Scores:
bonds:      0.0098544
angles:     0.120821
torsions:   N/A 
planes:     N/A 
non-bonded: 0
chiral vol: 0.139004
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 14.111
debug:: restraints results 1 4 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_3ins-6B-3.0-no-peptide-D.pdb_Fri_Sep_13_04:44:18_2013_modification_0.pdb.gz
INFO:: replace_coords: 18 atoms updated.
Symmetry available for this molecule
created 11 bond       restraints 
created 15 angle      restraints 
created 1 plane      restraints 
created 1 chiral vol restraints 
created 28 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 8784.3
    Initial RMS Z values
bonds:      1.1515
angles:     0.847578
torsions:   N/A 
planes:     3.05577
non-bonded: 116.199
chiral vol: 0.757848
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 63) at -272.29
    Final Estimated RMS Z Scores:
bonds:      0.260688
angles:     0.23195
torsions:   N/A 
planes:     0.209858
non-bonded: 0.00234627
chiral vol: 0.0806383
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 14.177
Refinement elapsed time: 0.024
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:18_2013_modification_0.pdb.gz
INFO:: replace_coords: 12 atoms updated.
created 12 bond       restraints 
created 15 angle      restraints 
created 1 plane      restraints 
created 1 chiral vol restraints 
created 29 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 3426.1
    Initial RMS Z values
bonds:      17.5578
angles:     0.23195
torsions:   N/A 
planes:     0.209858
non-bonded: 0
chiral vol: 0.0806383
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 31) at -313.089
    Final Estimated RMS Z Scores:
bonds:      0.0783225
angles:     0.100718
torsions:   N/A 
planes:     0.267083
non-bonded: 0
chiral vol: 0.018268
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 14.214
Refinement elapsed time: 0.024
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:18_2013_modification_1.pdb.gz
INFO:: replace_coords: 12 atoms updated.
 -- new structure created
SUMMARY:: rc CIFRC_Ok or newly created. 
Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb
 PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 49 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "ACT"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ACT.cif
There are 2 data in /home/emsley/data/greg-data/libcheck_ACT.cif
Welcome to Coot
WARNING:: bond_restraint_length 4 should be 5
created 5 bond       restraints 
created 9 angle      restraints 
created 1 plane      restraints 
created 0 chiral vol restraints 
created 15 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 10588.6
    Initial RMS Z values
bonds:      0.0119892
angles:     0.00653967
torsions:   N/A 
planes:     0
non-bonded: 755.759
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 13) at -79.5267
    Final Estimated RMS Z Scores:
bonds:      0.0186632
angles:     0.103515
torsions:   N/A 
planes:     0.0257578
non-bonded: 0
chiral vol: N/A 
rama plot:  N/A 
start_pos:  N/A 
 SUCCESS
 TIME:: (dragged refinement): 15
Refinement elapsed time: 0.049
INFO:: backup file coot-backup/_home_emsley_data_greg-data_monomer-ACT.pdb_Fri_Sep_13_04:44:19_2013_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 50 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_0.pdb.gz
istat: ; 1
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_1.pdb.gz
INFO:: Removing CIS peptide from PDB header: A 26 A 27 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_2.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_3.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_5.pdb.gz
INFO:: Removing CIS peptide from PDB header: B 26 B 27 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_6.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_7.pdb.gz
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:20_2013_modification_0.pdb.gz
INFO:: replace_coords: 1465 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 53 read successfully
DEBUG:: there were 0 types with no dictionary 
in new_molecule_by_residue_type_selection Something bad happened - No residues selected
in new_molecule_by_residue_type_selection Something bad happened - No residues selected
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:21_2013_modification_0.pdb.gz
oops! in rotamer::GetResidue() No tree in restraint
oops! in rotamer::GetResidue() No tree in restraint
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 54 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m-85" prob: 44%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "t80" prob: 33%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "p90" prob: 13%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%]
INFO:: [spec: 1 "A" 28 ""] [state: 1 name: "m -30 " prob: 9%]
Reading coordinate file: /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb
 PDB file /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 50/87
Molecule 55 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: aligning to mol number 55chain: A

-------------------------------------------------
        chain A
-------------------------------------------------
INFO:: input model  sequence: GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID
INFO:: input target sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
>  /home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb
---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID
> target seq: 
DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID
INFO:: alignment score 163.5
INFO:: backup file coot-backup/_home_emsley_data_greg-data_rnase-A-needs-an-insertion.pdb_Fri_Sep_13_04:44:22_2013_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: 4 "A" 1 ""] -> ASP
      [spec: 4 "A" 2 ""] -> VAL
      [spec: 4 "A" 3 ""] -> SER
      [spec: 4 "A" 11 ""] -> LEU
      [spec: 4 "A" 12 ""] -> PRO
      [spec: 4 "A" 13 ""] -> PRO
      [spec: 4 "A" 62 ""] -> PRO
      [spec: 4 "A" 63 ""] -> GLY
   Deletions:
      [spec: 4 "A" 24 ""]
      [spec: 4 "A" 33 ""]
   Mutations:
apply resno updates... 
Applied 3 insertions 
Applied 0 mutations 
Applied 2 deletions 
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 56 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:23_2013_modification_0.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 57 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:24_2013_modification_0.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/pdb3hfl.ent
 PDB file /home/emsley/data/greg-data/pdb3hfl.ent has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: NCS chain comparison 15/212
INFO:: NCS chain comparison 7/212
INFO:: NCS chain comparison 10/215
Molecule 58 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "PCA"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PCA.cif
valid_labels(/home/emsley/data/greg-data/3hfl_sigmaa.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.025 seconds to read MTZ file
INFO:: 0.007 seconds to initialize map
INFO:: 0.012 seconds for FFT
INFO:: 0.001 seconds for statistics
      Map mean: ........ 2.00384e-11
      Map sigma: ....... 0.260405
      Map maximum: ..... 1.71787
      Map minimum: ..... -1.03389
INFO:: 0.009 seconds for contour map
INFO:: 0.054 seconds in total
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Fri_Sep_13_04:44:25_2013_modification_0.pdb.gz
INFO:: replace_coords: 7 atoms updated.
Fitting score for best rotamer: 5.83361
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb3hfl.ent_Fri_Sep_13_04:44:25_2013_modification_1.pdb.gz
INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.0120681
    rms devi: 0.0134464
    max devi: 0.0214179
    min devi: 0.00385596
INFO:: 5 matched atoms had: 
   mean devi: 0.270216
    rms devi: 0.335002
    max devi: 0.536002
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.26738
    rms devi: 0.322791
    max devi: 0.495136
    min devi: 0.112289
INFO:: 5 matched atoms had: 
   mean devi: 0.270247
    rms devi: 0.335033
    max devi: 0.536044
    min devi: 0.0847029
INFO:: 5 matched atoms had: 
   mean devi: 0.267411
    rms devi: 0.322823
    max devi: 0.495177
    min devi: 0.112221
INFO:: 5 matched atoms had: 
   mean devi: 0.011982
    rms devi: 0.013349
    max devi: 0.0212578
    min devi: 0.0038732
INFO:: 5 matched atoms had: 
   mean devi: 0.000242576
    rms devi: 0.000242751
    max devi: 0.000256671
    min devi: 0.000231275
INFO:: 5 matched atoms had: 
   mean devi: 0.270185
    rms devi: 0.334971
    max devi: 0.535961
    min devi: 0.0845571
INFO:: 5 matched atoms had: 
   mean devi: 0.267349
    rms devi: 0.322759
    max devi: 0.495094
    min devi: 0.112357
INFO:: 5 matched atoms had: 
   mean devi: 6.9313e-05
    rms devi: 6.93629e-05
    max devi: 7.33402e-05
    min devi: 6.60841e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.0120334
    rms devi: 0.0134072
    max devi: 0.0213538
    min devi: 0.00386188
INFO:: 5 matched atoms had: 
   mean devi: 0.000138622
    rms devi: 0.000138721
    max devi: 0.000146676
    min devi: 0.000132164
INFO:: 5 matched atoms had: 
   mean devi: 0.011999
    rms devi: 0.0133684
    max devi: 0.0212898
    min devi: 0.0038691
INFO:: 5 matched atoms had: 
   mean devi: 0.267426
    rms devi: 0.322839
    max devi: 0.495197
    min devi: 0.112187
INFO:: 5 matched atoms had: 
   mean devi: 0.270294
    rms devi: 0.335079
    max devi: 0.536106
    min devi: 0.0848122
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:44:25_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:44:25_2013_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:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.0120681
    rms devi: 0.0134464
    max devi: 0.0214179
    min devi: 0.00385596
INFO:: 5 matched atoms had: 
   mean devi: 0.270216
    rms devi: 0.335002
    max devi: 0.536002
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.26738
    rms devi: 0.322791
    max devi: 0.495136
    min devi: 0.112289
INFO:: 5 matched atoms had: 
   mean devi: 0.270247
    rms devi: 0.335033
    max devi: 0.536044
    min devi: 0.0847029
INFO:: 5 matched atoms had: 
   mean devi: 0.267411
    rms devi: 0.322823
    max devi: 0.495177
    min devi: 0.112221
INFO:: 5 matched atoms had: 
   mean devi: 0.011982
    rms devi: 0.013349
    max devi: 0.0212578
    min devi: 0.0038732
INFO:: 5 matched atoms had: 
   mean devi: 0.000242576
    rms devi: 0.000242751
    max devi: 0.000256671
    min devi: 0.000231275
INFO:: 5 matched atoms had: 
   mean devi: 0.270185
    rms devi: 0.334971
    max devi: 0.535961
    min devi: 0.0845571
INFO:: 5 matched atoms had: 
   mean devi: 0.267349
    rms devi: 0.322759
    max devi: 0.495094
    min devi: 0.112357
INFO:: 5 matched atoms had: 
   mean devi: 6.9313e-05
    rms devi: 6.93629e-05
    max devi: 7.33402e-05
    min devi: 6.60841e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.0120334
    rms devi: 0.0134072
    max devi: 0.0213538
    min devi: 0.00386188
INFO:: 5 matched atoms had: 
   mean devi: 0.000138622
    rms devi: 0.000138721
    max devi: 0.000146676
    min devi: 0.000132164
INFO:: 5 matched atoms had: 
   mean devi: 0.011999
    rms devi: 0.0133684
    max devi: 0.0212898
    min devi: 0.0038691
INFO:: 5 matched atoms had: 
   mean devi: 0.267426
    rms devi: 0.322839
    max devi: 0.495197
    min devi: 0.112187
INFO:: 5 matched atoms had: 
   mean devi: 0.270294
    rms devi: 0.335079
    max devi: 0.536106
    min devi: 0.0848122
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:44:25_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:44:25_2013_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:: 5 matched atoms had: 
   mean devi: 0.00589883
    rms devi: 0.00670957
    max devi: 0.0101325
    min devi: 0.00258111
INFO:: 5 matched atoms had: 
   mean devi: 0.00725623
    rms devi: 0.00778801
    max devi: 0.0125644
    min devi: 0.00456024
INFO:: 5 matched atoms had: 
   mean devi: 0.271793
    rms devi: 0.336384
    max devi: 0.533839
    min devi: 0.0878288
INFO:: 5 matched atoms had: 
   mean devi: 0.26776
    rms devi: 0.326512
    max devi: 0.505569
    min devi: 0.10459
INFO:: 5 matched atoms had: 
   mean devi: 0.271823
    rms devi: 0.336416
    max devi: 0.53388
    min devi: 0.0879009
INFO:: 5 matched atoms had: 
   mean devi: 0.267791
    rms devi: 0.326544
    max devi: 0.505617
    min devi: 0.104522
INFO:: 5 matched atoms had: 
   mean devi: 0.00717866
    rms devi: 0.00770023
    max devi: 0.0124098
    min devi: 0.00457508
INFO:: 5 matched atoms had: 
   mean devi: 0.00574436
    rms devi: 0.00657052
    max devi: 0.0099594
    min devi: 0.0024248
INFO:: 5 matched atoms had: 
   mean devi: 0.271762
    rms devi: 0.336353
    max devi: 0.533797
    min devi: 0.0877567
INFO:: 5 matched atoms had: 
   mean devi: 0.267729
    rms devi: 0.326479
    max devi: 0.505521
    min devi: 0.104657
INFO:: 5 matched atoms had: 
   mean devi: 0.00585391
    rms devi: 0.00666923
    max devi: 0.0100827
    min devi: 0.00253528
INFO:: 5 matched atoms had: 
   mean devi: 0.00722485
    rms devi: 0.00775255
    max devi: 0.0125025
    min devi: 0.00456535
INFO:: 5 matched atoms had: 
   mean devi: 0.00580961
    rms devi: 0.00662938
    max devi: 0.0100332
    min devi: 0.00249036
INFO:: 5 matched atoms had: 
   mean devi: 0.00719394
    rms devi: 0.00771755
    max devi: 0.0124407
    min devi: 0.00457156
INFO:: 5 matched atoms had: 
   mean devi: 0.267807
    rms devi: 0.326561
    max devi: 0.505641
    min devi: 0.104488
INFO:: 5 matched atoms had: 
   mean devi: 0.27187
    rms devi: 0.336463
    max devi: 0.533942
    min devi: 0.088009
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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:: 5 matched atoms had: 
   mean devi: 0.00589883
    rms devi: 0.00670957
    max devi: 0.0101325
    min devi: 0.00258111
INFO:: 5 matched atoms had: 
   mean devi: 0.00725623
    rms devi: 0.00778801
    max devi: 0.0125644
    min devi: 0.00456024
INFO:: 5 matched atoms had: 
   mean devi: 0.271793
    rms devi: 0.336384
    max devi: 0.533839
    min devi: 0.0878288
INFO:: 5 matched atoms had: 
   mean devi: 0.26776
    rms devi: 0.326512
    max devi: 0.505569
    min devi: 0.10459
INFO:: 5 matched atoms had: 
   mean devi: 0.271823
    rms devi: 0.336416
    max devi: 0.53388
    min devi: 0.0879009
INFO:: 5 matched atoms had: 
   mean devi: 0.267791
    rms devi: 0.326544
    max devi: 0.505617
    min devi: 0.104522
INFO:: 5 matched atoms had: 
   mean devi: 0.00717866
    rms devi: 0.00770023
    max devi: 0.0124098
    min devi: 0.00457508
INFO:: 5 matched atoms had: 
   mean devi: 0.00574436
    rms devi: 0.00657052
    max devi: 0.0099594
    min devi: 0.0024248
INFO:: 5 matched atoms had: 
   mean devi: 0.271762
    rms devi: 0.336353
    max devi: 0.533797
    min devi: 0.0877567
INFO:: 5 matched atoms had: 
   mean devi: 0.267729
    rms devi: 0.326479
    max devi: 0.505521
    min devi: 0.104657
INFO:: 5 matched atoms had: 
   mean devi: 0.00585391
    rms devi: 0.00666923
    max devi: 0.0100827
    min devi: 0.00253528
INFO:: 5 matched atoms had: 
   mean devi: 0.00722485
    rms devi: 0.00775255
    max devi: 0.0125025
    min devi: 0.00456535
INFO:: 5 matched atoms had: 
   mean devi: 0.00580961
    rms devi: 0.00662938
    max devi: 0.0100332
    min devi: 0.00249036
INFO:: 5 matched atoms had: 
   mean devi: 0.00719394
    rms devi: 0.00771755
    max devi: 0.0124407
    min devi: 0.00457156
INFO:: 5 matched atoms had: 
   mean devi: 0.267807
    rms devi: 0.326561
    max devi: 0.505641
    min devi: 0.104488
INFO:: 5 matched atoms had: 
   mean devi: 0.27187
    rms devi: 0.336463
    max devi: 0.533942
    min devi: 0.088009
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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:: backup file coot-backup/Ideal-A-form-DNA_Fri_Sep_13_04:44:25_2013_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
Symmetry available for this molecule
INFO:: mutate 32 A to a LYS
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:25_2013_modification_0.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/some-waters-with-ter.pdb
 PDB file /home/emsley/data/greg-data/some-waters-with-ter.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 65 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_some-waters-with-ter.pdb_Fri_Sep_13_04:44:26_2013_modification_0.pdb.gz
1/D/79 {HOH}/ O   altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule
Reading coordinate file: /home/emsley/data/greg-data/tm+some-waters.pdb
 PDB file /home/emsley/data/greg-data/tm+some-waters.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 66 read successfully
DEBUG:: there were 0 types with no dictionary 
Protein centre at: xyz = (     41.57,     8.745,     12.89)
using sigma cut off 2
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.311501
INFO:: Using density cut-off: 0.623002 (2 sigma)  (mean -0.0338214 stdev: 0.146177)
INFO:: Using water to protein distance limits: 1.5 3.6
Finding clusters...done
-------------------------------------------------------------
INFO:: cluster at xyz = (     59.88,     3.015,    -4.288) is too big to be water
INFO:: cluster at xyz = (     70.02,     19.08,     18.63) is too big to be water
INFO:: cluster at xyz = (        53,     9.031,     20.13) is too big to be water
INFO:: found 62 waters in water fitting
Done - back from lig.water_fit()
DEBUG::  new_waters_mol_flag: 0
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tm+some-waters.pdb_Fri_Sep_13_04:44:27_2013_modification_0.pdb.gz
INFO:: Adding to solvent chain: D
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 67 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_0.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_1.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_2.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_3.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_4.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_5.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_6.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_7.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_8.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_9.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_10.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_11.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_12.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_13.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_14.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_15.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_16.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_17.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_18.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_19.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_20.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_21.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_22.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_23.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_24.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_25.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_26.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_27.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_28.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_29.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_30.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_31.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_32.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_33.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_34.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_35.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_36.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_37.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_38.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_39.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_40.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_41.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_42.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_43.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_44.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_45.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_46.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_47.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_48.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_49.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_50.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_51.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_52.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_53.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_54.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_55.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_56.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_57.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_58.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_59.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_60.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_61.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_62.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_63.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_64.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_65.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_66.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_67.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_68.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_69.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_70.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_71.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_72.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_73.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_74.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_75.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_76.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_77.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_78.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_79.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_80.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_81.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_82.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_83.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_84.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_85.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_86.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_87.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_88.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_89.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_90.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_91.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_92.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_93.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_94.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_95.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_96.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_97.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_98.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:27_2013_modification_99.pdb.gz
0//-32767 {MG}/MG   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule
851 0.687578678131104 0.801753640174866 0.738103628158569 1.06824910640717 1.01713156700134 1.01199650764465 0.822739899158478)  low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0)
   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: (-0.893179178237915 -0.947303891181946 -1.18386626243591 -1.29074656963348 -1.08600687980652 -0.827113330364227 -0.848896384239197 -0.693203151226044 -0.970726788043976 -0.553648889064789)
PASS: Mask and difference map
Entered testcase - Simple Averaged maps
  INFO:: map sigmas: normal 0.311048001050949 and diff-map: 0.00108590547461063
PASS: Simple Averaged maps
Entered testcase - Make a glycosidic linkage
   bond-length: 2.97694066606539: 
   bond-length: 1.44039386011154: 
PASS: Make a glycosidic linkage
Entered testcase - Test for flying hydrogens on undo
PASS: Test for flying hydrogens on undo
Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0
PASS: Test for mangling of hydrogen names from a PDB v 3.0
Entered testcase - correct matching dictionary names from test name
PASS: correct matching dictionary names from test name
Entered testcase - update monomer restraints
   Bond-length: 2.84994989549065: 
   pass intermediate 2.8 tolerance test
  OK plane atom " CB "
   Bond-length: 1.51394823659121: 
PASS: update monomer restraints
Entered testcase - Write mmCIF restraints correctly
PASS: Write mmCIF restraints correctly
Entered testcase - Refinement OK with zero bond esd
PASS: Refinement OK with zero bond esd
Entered testcase - Change Chain IDs and Chain Sorting
PASS: Change Chain IDs and Chain Sorting
Entered testcase - Replace Fragment
   distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327)
PASS: Replace Fragment
Entered testcase - Residues in Region of Residue
   found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 ""))
   found 0 neighbours ()
PASS: Residues in Region of Residue
Entered testcase - Residues in region of a point
PASS: Residues in region of a point
Entered testcase - Empty molecule on type selection
PASS: Empty molecule on type selection
Entered testcase - Set Rotamer
PASS: Set Rotamer
Entered testcase - Rotamer names and scores are correct
   Rotamer 0 : "m-85" 100.0 
   Rotamer 1 : "t80" 90.1668395996094 
   Rotamer 2 : "p90" 50.7077865600586 
   Rotamer 3 : "m -30 " 21.4231548309326 
   Rotamer 4 : "m -30 " 21.4231548309326 
PASS: Rotamer names and scores are correct
Entered testcase - Align and mutate a model with deletions
    ::::: (55 "A" 1 "") #f #f
    ::::: (55 "A" 4 "") #t #t
    ::::: (55 "A" 59 "") #t #t
    ::::: (55 "A" 60 "") #f #f
    ::::: (55 "A" 61 "") #f #f
    ::::: (55 "A" 92 "") #t #t
    ::::: (55 "A" 94 "") #f #f
PASS: Align and mutate a model with deletions
Entered testcase - renumbered residues should be in seqnum order
PASS: renumbered residues should be in seqnum order
Entered testcase - Autofit Rotamer on Residues with Insertion codes
PASS: Autofit Rotamer on Residues with Insertion codes
Entered testcase - RNA base has correct residue type after mutation
  mutated base to type "C" - was "A" 
  mutated base to type "Cr" - was "A" 
PASS: RNA base has correct residue type after mutation
Entered testcase - DNA bases are the correct residue type after mutation
  mutated base to type "DC"
  mutated base to type "DG"
  mutated base to type "DA"
  mutated base to type "DT"
  mutated base to type "Cd"
  mutated base to type "Gd"
  mutated base to type "Ad"
  mutated base to type "Td"
PASS: DNA bases are the correct residue type after mutation
Entered testcase - SegIDs are correct after mutate
PASS: SegIDs are correct after mutate
Entered testcase - TER on water chain is removed on adding a water by hand
PASS: TER on water chain is removed on adding a water by hand
Entered testcase - TER on water chain is removed on adding waters automatically
PASS: TER on water chain is removed on adding waters automatically
Entered testcase - Adding atoms to Many-Chained Molecule
PASS: Adding atoms to Many-Chained Molecule
Entered tReading coordinate file: /home/emsley/data/greg-data/water-test-no-cell.pdb
 PDB file /home/emsley/data/greg-data/water-test-no-cell.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 68 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_water-test-no-cell.pdb_Fri_Sep_13_04:44:32_2013_modification_0.pdb.gz
No symmetry available
INFO:: moved 0 water molecules
Reading coordinate file: /home/emsley/data/greg-data/pathological-water-test.pdb
 PDB file /home/emsley/data/greg-data/pathological-water-test.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 69 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pathological-water-test.pdb_Fri_Sep_13_04:44:33_2013_modification_0.pdb.gz
INFO:: moved 181 water molecules
Symmetry available for this molecule
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.025 seconds to read MTZ file
INFO:: 0.012 seconds to initialize map
INFO:: 0.016 seconds for FFT
INFO:: 0.001 seconds for statistics
      Map mean: ........ 1.06932e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.019 seconds for contour map
INFO:: 0.073 seconds in total
INFO:: Masking around 58 atoms
fitting terminal residue with 100 random trials
INFO:: Fitting terminal residue  without individual rigid body fitting.
 A 94 ALA  N   :: xyz = (     58.52,     2.828,    -1.801)
 A 94 ALA  C   :: xyz = (     59.88,     1.672,    -3.498)
 A 94 ALA  CA  :: xyz = (      59.8,     2.182,    -2.063)
 A 94 ALA  O   :: xyz = (     58.86,     1.305,    -4.092)
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:33_2013_modification_0.pdb.gz
Symmetry available for this molecule
WARNING:: failed to find master_chain_id "A" in 0 NCS ghosts
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 73 read successfully
DEBUG:: there were 0 types with no dictionary 
0//-32767 {HOH}/ O   altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain)
1/C/2 {HOH}/ O   altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/C/3 {HOH}/ O   altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/C/4 {HOH}/ O   altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/C/5 {HOH}/ O   altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/16 {HOH}/ O   altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/17 {HOH}/ O   altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/18 {HOH}/ O   altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/19 {HOH}/ O   altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/20 {HOH}/ O   altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/21 {HOH}/ O   altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/22 {HOH}/ O   altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/23 {HOH}/ O   altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/24 {HOH}/ O   altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule
1/D/25 {HOH}/ O   altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule
Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent
 PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 74 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "TAR"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TAR.cif
Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb
 PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 75 read successfully
DEBUG:: there were 0 types with no dictionary 
Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb
 PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 76 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "NPO"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NPO.cif
-X,-X+Y,-Z+1/3 ->
-1 0 0
-1 1 0
0 0 -1
translations: 0 0 0.333333
pre-trans: 0 0 0
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Matching/moving molecule number 79 to 78
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__home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:36_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal 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)
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 80 read successfully
DEBUG:: there were 0 types with no dictionary 
Reading coordinate file: /home/emsley/data/greg-data/pdb1py3.ent
 PDB file /home/emsley/data/greg-data/pdb1py3.ent has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 91/204
INFO:: NCS chain comparison 90/204
INFO:: NCS chain comparison 175/179
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain B"
Molecule 81 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: spacegroup: P 21 21 21
INFO:: spacegroup: C 1 2 1
INFO:: Matching/moving molecule number 80 to 81
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/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:37_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal 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
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 82 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:44:38_2013_modification_0.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 83 read successfully
DEBUG:: there were 0 types with no dictionary 
Reading coordinate file: /home/emsley/data/greg-data/2goz-manip.pdb
 PDB file /home/emsley/data/greg-data/2goz-manip.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 7 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/85
Molecule 84 read successfully
DEBUG:: there were 7 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "GDP"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GDP.cif
INFO:: using standard CCP4 Refmac dictionary to search for "Gr"
INFO:: using standard CCP4 Refmac dictionary to search for "Ar"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif
INFO:: using standard CCP4 Refmac dictionary to search for "Ur"
INFO:: using standard CCP4 Refmac dictionary to search for "Cr"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif
INFO:: using standard CCP4 Refmac dictionary to search for "OMC"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/o/OMC.cif
INFO:: using standard CCP4 Refmac dictionary to search for "5BU"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/5/5BU.cif
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
estcase - Arrange waters round protein
PASS: Arrange waters round protein
Entered testcase - Correct Segid After Add Terminal Residue
PASS: Correct Segid After Add Terminal Residue
Entered testcase - Correct Segid after NCS residue range copy
PASS: Correct Segid after NCS residue range copy
Entered testcase - Merge Water Chains
PASS: Merge Water Chains
Entered testcase - Consolidated merge
-------- starting chain list ----------- 
DEBUG:: (chain-ids imol) is ("A" "B" "C" "D" "")
DEBUG:: chain-list is ("A" "B" "C" "D" "" "E" "F" "G" "H" "I" "J" "K")
PASS: Consolidated merge
Entered testcase - LSQ by atom
PASS: LSQ by atom
Entered testcase - LSQing changes the space-group and cell to that of the reference molecule
PASS: LSQing changes the space-group and cell to that of the reference molecule
Entered testcase - set-residue-name sets the correct residue
PASS: set-residue-name sets the correct residue
Entered testcase - fit-protein-make-specs makes all specs
   specs: 189 ((83 "A" 1 "") (83 "A" 2 "") (83 "A" 3 "") (83 "A" 4 "") (83 "A" 5 "") (83 "A" 6 "") (83 "A" 7 "") (83 "A" 8 "") (83 "A" 9 "") (83 "A" 10 "") (83 "A" 11 "") (83 "A" 12 "") (83 "A" 13 "") (83 "A" 14 "") (83 "A" 15 "") (83 "A" 16 "") (83 "A" 17 "") (83 "A" 18 "") (83 "A" 19 "") (83 "A" 20 "") (83 "A" 21 "") (83 "A" 22 "") (83 "A" 23 "") (83 "A" 24 "") (83 "A" 25 "") (83 "A" 26 "") (83 "A" 27 "") (83 "A" 28 "") (83 "A" 29 "") (83 "A" 30 "") (83 "A" 31 "") (83 "A" 32 "") (83 "A" 33 "") (83 "A" 34 "") (83 "A" 35 "") (83 "A" 36 "") (83 "A" 37 "") (83 "A" 38 "") (83 "A" 39 "") (83 "A" 40 "") (83 "A" 41 "") (83 "A" 42 "") (83 "A" 43 "") (83 "A" 44 "") (83 "A" 45 "") (83 "A" 46 "") (83 "A" 47 "") (83 "A" 48 "") (83 "A" 49 "") (83 "A" 50 "") (83 "A" 51 "") (83 "A" 52 "") (83 "A" 53 "") (83 "A" 54 "") (83 "A" 55 "") (83 "A" 56 "") (83 "A" 57 "") (83 "A" 58 "") (83 "A" 59 "") (83 "A" 60 "") (83 "A" 61 "") (83 "A" 62 "") (83 "A" 63 "") (83 "A" 64 "") (83 "A" 65 "") (83 "A" 66 "") (83 "A" 67 "") (83 "A" 68 "") (83 "A" 69 "") (83 "A" 70 "") (83 "A" 71 "") (83 "A" 72 "") (83 "A" 73 "") (83 "A" 74 "") (83 "A" 75 "") (83 "A" 76 "") (83 "A" 77 "") (83 "A" 78 "") (83 "A" 79 "") (83 "A" 80 "") (83 "A" 81 "") (83 "A" 82 "") (83 "A" 83 "") (83 "A" 84 "") (83 "A" 85 "") (83 "A" 86 "") (83 "A" 87 "") (83 "A" 88 "") (83 "A" 89 "") (83 "A" 90 "") (83 "A" 91 "") (83 "A" 92 "") (83 "A" 93 "") (83 "B" 1 "") (83 "B" 2 "") (83 "B" 3 "") (83 "B" 4 "") (83 "B" 5 "") (83 "B" 6 "") (83 "B" 7 "") (83 "B" 8 "") (83 "B" 9 "") (83 "B" 10 "") (83 "B" 11 "") (83 "B" 12 "") (83 "B" 13 "") (83 "B" 14 "") (83 "B" 15 "") (83 "B" 16 "") (83 "B" 17 "") (83 "B" 18 "") (83 "B" 19 "") (83 "B" 20 "") (83 "B" 21 "") (83 "B" 22 "") (83 "B" 23 "") (83 "B" 24 "") (83 "B" 25 "") (83 "B" 26 "") (83 "B" 27 "") (83 "B" 28 "") (83 "B" 29 "") (83 "B" 30 "") (83 "B" 31 "") (83 "B" 32 "") (83 "B" 33 "") (83 "B" 34 "") (83 "B" 35 "") (83 "B" 36 "") (83 "B" 37 "") (83 "B" 38 "") (83 "B" 39 "") (83 "B" 40 "") (83 "B" 41 "") (83 "B" 42 "") (83 "B" 43 "") (83 "B" 44 "") (83 "B" 45 "") (83 "B" 46 "") (83 "B" 47 "") (83 "B" 48 "") (83 "B" 49 "") (83 "B" 50 "") (83 "B" 51 "") (83 "B" 52 "") (83 "B" 53 "") (83 "B" 54 "") (83 "B" 55 "") (83 "B" 56 "") (83 "B" 57 "") (83 "B" 58 "") (83 "B" 59 "") (83 "B" 60 "") (83 "B" 61 "") (83 "B" 62 "") (83 "B" 63 "") (83 "B" 64 "") (83 "B" 65 "") (83 "B" 66 "") (83 "B" 67 "") (83 "B" 68 "") (83 "B" 69 "") (83 "B" 70 "") (83 "B" 71 "") (83 "B" 72 "") (83 "B" 73 "") (83 "B" 74 "") (83 "B" 75 "") (83 "B" 76 "") (83 "B" 77 "") (83 "B" 78 "") (83 "B" 79 "") (83 "B" 80 "") (83 "B" 81 "") (83 "B" 82 "") (83 "B" 83 "") (83 "B" 84 "") (83 "B" 85 "") (83 "B" 86 "") (83 "B" 87 "") (83 "B" 88 "") (83 "B" 89 "") (83 "B" 90 "") (83 "B" 91 "") (83 "B" 92 "") (83 "B" 93 "") (83 "B" 94 "") (83 "B" 95 "") (83 "B" 96 ""))
PASS: fit-protein-make-specs makes all specs
Entered testcase - Phosphate distance in pucker analysis is sane
PASS: Phosphate distance in pucker analysis is sane
Ended 01-pdb+mtz.scm
Running 02-shelx.scm ...
Entered testcase - Read small molecule .res file
PASS: Read small molecule .res file
EMolecule 85 read successfully
LATT LINE: LATT -2
SFAC LINE: SFAC C H N O CO
INFO:: CELL set to 34.3243 34.3243 11.0887 90 90 90
READ-INS:: Spacegroup: "I 41 2 2"
INFO:: chain has 2 residues
Symmetry available for this molecule
Molecule 86 read successfully
INFO:: spacegroup: I 41 2 2
LATT LINE: LATT -2
SFAC LINE: SFAC  C  H  N  O  S
INFO:: CELL set to 77.726 77.726 77.726 90 90 90
READ-INS:: Spacegroup: "I 21 3"
INFO:: chain has 121 residues
Symmetry available for this molecule
Molecule 87 read successfully
DEBUG:: space group initialised with symbol "I 21 3"
Map statistics: mean: -5.07009e-05 st.d: 0.305174
Map statistics: min: -0.781031, max: 6.07907
-0.609528    4955
-0.266523    80201
0.0764816    136171
0.419487    11448
0.762492    4907
  1.1055    2959
  1.4485    1483
 1.79151    595
 2.13451    234
 2.47752    108
 2.82052    34
 3.16353    23
 3.50653    8
 3.84954    10
 4.19254    7
 4.53555    3
 4.87855    2
 5.22156    1
 5.56456    0
 5.90757    1
 6.25057    0
Map statistics: mean: -1.00547e-05 st.d: 0.0468085
Map statistics: min: -0.211523, max: 0.648623
-0.19002    55
-0.147012    996
-0.104005    7933
-0.0609978    37110
-0.0179905    84420
0.0250169    76364
0.0680242    29138
0.111032    5797
0.154039    1047
0.197046    210
0.240053    40
0.283061    21
0.326068    4
0.369075    3
0.412083    3
 0.45509    3
0.498097    2
0.541105    2
0.584112    0
0.627119    2
0.670127    0
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
INFO:: spacegroup: I 21 3
WARNING:: invalid molecule (204050) for write_shelx_ins_file
ERROR transfering AFIX back
WARNING:: failed to get AFIX handle for "" 1 "ASP" " N  "
WARNING:: failed to get AFIX handle for "" 1 "ASP" " CA "
WARNING:: failed to get AFIX handle for "" 1 "ASP" " CB "
WARNING:: failed to get AFIX handle for "" 1 "ASP" " CG "
WARNING:: failed to get AFIX handle for "" 1 "ASP" " OD1"
WARNING:: failed to get AFIX handle for "" 1 "ASP" " OD2"
WARNING:: failed to get AFIX handle for "" 1 "ASP" " C  "
WARNING:: failed to get AFIX handle for "" 1 "ASP" " O  "
WARNING:: failed to get AFIX handle for "" 2 "VAL" " N  "
WARNING:: failed to get AFIX handle for "" 2 "VAL" " CA "
INFO:: SHELXL file rnase.ins written.
Symmetry available for this molecule
Symmetry available for this molecule
INFO:: Masking around 32 atoms
fitting terminal residue with 100 random trials
INFO:: Fitting terminal residue  without individual rigid body fitting.
 B 2021 ALA  N   :: xyz = (    -10.55,     18.01,      59.5)
 B 2021 ALA  C   :: xyz = (    -9.167,     19.73,     60.59)
 B 2021 ALA  CA  :: xyz = (     -10.5,     18.99,     60.57)
 B 2021 ALA  O   :: xyz = (    -8.111,     19.11,     60.74)
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: mutating residue in add_cb_to_terminal_res
INFO:: backup file coot-backup/atom_selection_from_insulin.res_Fri_Sep_13_04:44:40_2013_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:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Fri_Sep_13_04:44:40_2013_modification_0.res
1/D/3069 {HOH}/ O   altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule
Protein centre at: xyz = (   -0.2998,      10.6,     57.56)
using sigma cut off 0.6
Calling lig.water_fit()
INFO:: find_clusters map_rms is 0.305174
INFO:: Using density cut-off: 0.183104 (0.6 sigma)  (mean -0.0203497 stdev: 0.111926)
INFO:: Using water to protein distance limits: 1.5 3.6
Finding clusters...done
-------------------------------------------------------------
INFO:: cluster at xyz = (    -4.859,      20.8,      69.7) is too big to be water
INFO:: cluster at xyz = (     4.249,    -1.354,     48.69) is too big to be water
INFO:: cluster at xyz = (   0.05491,      16.3,     69.67) is too big to be water
INFO:: cluster at xyz = (     15.59,      8.13,     53.24) is too big to be water
INFO:: cluster at xyz = (     20.55,     4.875,     65.84) is too big to be water
INFO:: cluster at xyz = (    -5.054,     9.822,     69.12) is too big to be water
INFO:: found 126 waters in water fitting
Done - back from lig.water_fit()
DEBUG::  new_waters_mol_flag: 0
INFO:: backup file coot-backup/_home_emsley_data_greg-data_insulin.res_Fri_Sep_13_04:44:40_2013_modification_1.res
ERROR transfering AFIX back
WARNING:: failed to get AFIX handle for "" 3069 "HOH" " O  "
INFO:: Adding to solvent chain: D
LATT LINE: LATT -1
SFAC LINE: SFAC  C  H  N  O  S  SE  CL
WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3:
INFO:: CELL set to 42.14 83.03 89.79 90 90 90
READ-INS:: Spacegroup: "P 21 21 21"
INFO:: chain has 5 residues
Symmetry available for this molecule
Molecule 92 read successfully
LATT LINE: LATT -1
SFAC LINE: SFAC C H N O MG CL
INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90
READ-INS:: Spacegroup: "P 1 21 1"
INFO:: chain has 23 residues
Symmetry available for this molecule
Molecule 93 read successfully
INFO:: SHELXL file new-horma.ins written.
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 94 read successfully
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 95 read successfully
INFO:: Creating directory coot-ccp4
ntered testcase - Read hollander small molecule .res file
PASS: Read hollander small molecule .res file
Entered testcase - read shelx insulin with fcf
PASS: read shelx insulin with fcf
Entered testcase - Write an INS from PDB test
PASS: Write an INS from PDB test
Entered testcase - new molecule by atom selection inherits shelx molecule flag
PASS: new molecule by atom selection inherits shelx molecule flag
Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy
PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy
Entered testcase - Add water to SHELX molecule
PASS: Add water to SHELX molecule
Entered testcase - Find Waters for a SHELXL molecule
PASS: Find Waters for a SHELXL molecule
Entered testcase - NPD Anisotropic Atom [Mitch Miller]
PASS: NPD Anisotropic Atom [Mitch Miller]
Entered testcase - close shelx molecules
PASS: close shelx molecules
Entered testcase - Aniso Bs in P21
b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) 
b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) 
PASS: Aniso Bs in P21
Entered testcase - Don't crash on reading a strange HAT file
PASS: Don't crash on reading a strange HAT file
Ended 02-shelx.scm
Running 03-ligand.scm ...
Entered testcase - Get monomer test
run-command-in-dir args: "coot-ccp4/" "libcheck" () ("N" "MON 3GP" "") "coot-libcheck-3GP.log" #t
:
:  --- LIBCHECK --- /Vers 5.2.00  ; 12.12.2011/
:
:
:  Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A :
:    N - means without DOC-file
:    Y - with new contents
:    A - means to keep old contents and add new information
:        with DOC-file program creates batch file: libcheck.bat
: _DOC:
:
: #
: #      Keywords:
: #
: #FILE_L:   < >  - additional library, " " means without this file
: #MON:      < >  - give info about this monomer
: #                 if = * , give list all monomers in the library
: #FILE_PDB: < >  - input PDB_file  ," " means without this file
: #FILE_SMILE: < >  - input SMILE_file  ," " means without this fil e
: #FILE_SDF:   < > - input SDF file, " " means without this file
: #FILE_MOL:   < > - input MOL (sybil), SDF, ODB (O) files
: #                   use keyword MON as compound_id
: #FILE_CIF: < >  - input CIFile    ," " means without this file
: #FILE_CSD: < >  - input CSD CIFile," " means without this file
: #HFLAG: <Y>/A/N - Y - hydrogen atoms where they are
: #                 A - with all hydrogen atoms
: #                 N - without hydrogen atoms
: #IND:    <N>/Y  - Y - create index of mon_lib.cif
: #                     output file: "new_mon_lib_ind.cif"
: #FILE_O: <libcheck > - output files /library,coords,ps/, name without
: #                      extention
: #FILE_L2:  < >  - additional library (FILE_L) will be added to this library
: #                 in this case program performs only adding
: #ANGLE:   <0.0> - rotation angle for picture ( around X )
: #LIST: <M>/S/L  - S short output, L - long, M - medium
: #REF:  <Y>/S,N,0 - 0 no refinement of new monomer
: #                  N only crd->ang and ang->crd
: #                  S plus torsion ref, Y plus restr.ref
: #
: #TEST:   <0>    - for program testing only
: #COOR: <N>/Y    - use Vobs from coords instead Videal
: #LCOOR: <Y>/N   - Y use coords from lib description
: #NODIST: <N>/Y  - Y not read the distributed library
: #                 (only with FILE_L)
: #SRCH: <N>/Y/0  - Y - global search, 0 - for MON from PDB_file
: #                 (only with NODIST = N)
:
: #---  type "keyword   parameters" and/or ---
: #---  press key "CR" to run program      ---
: --> --> MON   : 3GP
: -------------
: -------------
: Keywords:
: HFLAG : Y
: COOR  : N
: LCOOR : Y
: SRCH  : N
: REF   : Y
: NODIST: N
:  NUMBER OF MONOMERS IN THE LIBRARY          : 11459
:                with complete description    : 11459
:  NUMBER OF MODIFICATIONS                    :    53
:  NUMBER OF LINKS                            :    66
:  I am reading libraries. Please wait.
:      - energy parameters
:      - monomer"s description (links & mod )
:  I am reading library. Please wait.
:      - monomer"s description
: * CIFile  : libcheck_3GP.cif
: * PDBfile : libcheck_3GP.pdb
: * Plotfile: libcheck_3GP.ps
: Output dictionary 
:    mmcif : libcheck.lib
:    odb   : libcheck.odb
INFO:: libcheck status: 0
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:<html> <!-- CCP4 HTML LOGFILE -->
:<hr>
:<!--SUMMARY_END--></FONT></B>
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:<pre>
: 
: ###############################################################
: ###############################################################
: ###############################################################
: ### CCP4 6.3: Refmac_5.7.0029     version 5.7.0029 : 25/06/12##
: ###############################################################
: User: emsley  Run date: 13/ 9/2013 Run time: 04:44:45 
:
:
: Please reference: Collaborative Computational Project, Number 4. 1994.
: "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
: as well as any specific reference in the program write-up.
:
:<!--SUMMARY_END--></FONT></B>
: $TEXT:Reference1: $$ Main reference $$ 
:   "REFMAC5 for the refinement of macromolecular crystal structures:"
:   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
:   Acta Crystallogr. D67, 355-367
:
: $$
: $SUMMARY :Reference1:  $$ Refmac: $$
: :TEXT:Reference1: $$
:
: $TEXT:Reference2: $$ Secondary reference $$ 
:   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
:   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
:   Acta Crystallogr. D53, 240-255
:   EU  Validation contract: BIO2CT-92-0524
:
: $$
: $SUMMARY :Reference2:  $$ Refmac: $$
: :TEXT:Reference2: $$
:
:  Data line--- MODE NEWENTRY
:  Data line--- END
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
:
:    ****                     Input and Default parameters#                      ****
:
:
:Input coordinate file.  Logical name - XYZIN actual file name  - coot-ccp4/libcheck_3GP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name - coot-ccp4/monomer-3GP.pdb
:
:  Refinement type                        : Idealisation
:
:
:    ****                           Makecif parameters                           ****
:
:Dictionary files for restraints : /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/mon*cif
:Parameters for new entry and VDW: /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif
:User supplied dictionary entries: coot-ccp4/libcheck_3GP.cif
:    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
:    Hydrogens will be restored in their riding positions
:    hydrogens will be written to the output file
:    Links between monomers will be checked. Only those links present in the coordinate file will be used
:    Standard sugar links will be analysed and used
:    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
:    Symmetry related links will be analysed and used
:    Cis peptides will be found and used automatically
:
:
:
:
:Monitoring style is "MEDIUM". Complete information will be printed out in the
:first and last cycle. In all other cycles minimum information will be printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will be printed out
:Distance outliers      10.000
:Angle outliers         10.000
:Torsion outliers       10.000
:Chiral volume outliers 10.000
:Plane outliers         10.000
:Non-bonding outliers   10.000
:---------------------------------------------------------------
:
: Input file :coot-ccp4/libcheck_3GP.pdb
:  NUMBER OF MONOMERS IN THE LIBRARY          : 11459
:                with complete description    : 11459
:  NUMBER OF MODIFICATIONS                    :    53
:  NUMBER OF LINKS                            :    66
:  I am reading libraries. Please wait.
:      - energy parameters
:      - monomer"s description (links & mod )
:
:FORMATTED      OLD     file opened on unit  45
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:Logical name: ATOMSF, Filename: /home/emsley/ccp4/ccp4-6.3.0/lib/data/atomsf.lib
:<!--SUMMARY_END--></FONT></B>
:
:
: Spacegroup information obtained from library file: 
: Logical Name: SYMINFO   Filename: /home/emsley/autobuild/installed-pre-release-gtk2-python/share/coot/syminfo.lib
:
:  WARNING: "SCALE" card is absent in input PDB file
:  Number of atoms    :      36
:  Number of residues :       1
:  Number of chains   :       1
:  I am reading library. Please wait.
:                mon_lib.cif
:  --------------------------------
:  --- title of input coord file ---
:
:  PDB_code:3GP
:  PDB_name:coords of 3GP from prog: libcheck
:  PDB_date:XX-XXX-XX
:  --------------------------------
:  Number of chains                  :       1
:  Total number of monomers          :       1
:  Number of atoms                   :      36
:  Number of missing atoms           :       0
:  Number of rebuilt atoms           :       0
:  Number of unknown atoms           :       0
:  Number of deleted atoms           :       0
:
:
: loop_
:     _atom_type_symbol
:     _atom_type_scat_Cromer_Mann_a1
:     _atom_type_scat_Cromer_Mann_b1
:     _atom_type_scat_Cromer_Mann_a2
:     _atom_type_scat_Cromer_Mann_b2
:     _atom_type_scat_Cromer_Mann_a3
:     _atom_type_scat_Cromer_Mann_b3
:     _atom_type_scat_Cromer_Mann_a4
:     _atom_type_scat_Cromer_Mann_b4
:     _atom_type_scat_Cromer_Mann_c
:
:
:  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
:  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
:  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
:  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
:  P      6.4345   1.9067   4.1791  27.1570   1.7800   0.5260   1.4908  68.1645   1.1149
:
:
: Number of distances         :           0
: Number of angles            :           0
: Number of torsions          :           0
: Number of planes            :           0
: Number of chirals           :           0
: Number of intervals         :           0
:--------------------------------------------------------------------------------
:---------------------------------------
:                        Standard  External       All
:                Bonds:        38         0        38
:               Angles:        66         0        66
:              Chirals:         4         0         4
:               Planes:         2         0         2
:             Torsions:        22         0        22
:---------------------------------------
:
:
:
:     CGMAT cycle number =      1
:
: function value    19446.416    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.030     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     4.292     3.000
:Bond angles  : others                            26     1.222     3.000
:Torsion angles, period  1. refined               15     3.618    15.000
:Torsion angles, period  1. others                 3     0.015    15.000
:Torsion angles, period  3. refined                4     5.039    15.000
:Chiral centres: refined atoms                     4     0.186     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.005     0.020
:VDW repulsions.others                             6     0.189     0.200
:VDW; torsion: refined_atoms                       7     0.281     0.200
:VDW; torsion.others                               4     0.224     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       19446.416       363.92786       19446.416    
:
:
:     CGMAT cycle number =      2
:
: function value    363.92786    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.081     0.020
:Bond distances: others                           12     0.013     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       363.92786       1259.5922       363.92786    
:
: fvalues    0.0000000       363.92786       483.19171       363.92786    
:
:
:     CGMAT cycle number =      3
:
: function value    343.50781    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.079     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       343.50781       293.11017       343.50781    
:
:
:     CGMAT cycle number =      4
:
: function value    293.11017    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.076     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Gamma decreased to   1.66446306E-02
:
:
: fvalues    0.0000000       293.11017       287.58200       293.11017    
:
:
:     CGMAT cycle number =      5
:
: function value    287.58200    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   1.66446306E-02
: Gamma decreased to   9.13148280E-03
:
:
: fvalues    0.0000000       287.58200       230.52641       287.58200    
:
:
:     CGMAT cycle number =      6
:
: function value    230.52641    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.13148280E-03
: Not converging with gamma equal   9.13148280E-03
: Trying gamma equal   4.66972217E-02
: Gamma decreased to   3.91840748E-02
:
:
: fvalues    0.0000000       230.52641       281.71072       230.52641    
:
: fvalues    0.0000000       230.52641       242.13728       230.52641    
:
:
:     CGMAT cycle number =      7
:
: function value    233.00272    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.91840748E-02
: Gamma decreased to   3.23539414E-02
:
:
: fvalues    0.0000000       233.00272       230.08240       233.00272    
:
:
:     CGMAT cycle number =      8
:
: function value    230.08240    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.23539414E-02
: Gamma decreased to   2.61447281E-02
:
:
: fvalues    0.0000000       230.08240       229.98131       230.08240    
:
:
:     CGMAT cycle number =      9
:
: function value    229.98131    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.61447281E-02
: Gamma decreased to   2.04999894E-02
:
:
: fvalues    0.0000000       229.98131       229.51228       229.98131    
:
:
:     CGMAT cycle number =     10
:
: function value    229.51228    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.04999894E-02
: Not converging with gamma equal   2.04999894E-02
: Trying gamma equal   4.87236828E-02
: Not converging with gamma equal   4.87236828E-02
: Trying gamma equal   7.97697455E-02
: Not converging with gamma equal   7.97697455E-02
: Trying gamma equal   0.11392042    
: Not converging with gamma equal   0.11392042    
: Trying gamma equal   0.15148616    
: Not converging with gamma equal   0.15148616    
: Trying gamma equal   0.19280848    
: Gamma decreased to   0.18454401    
:
:
: fvalues    0.0000000       229.51228       229.47993       229.51228    
:
:
:     CGMAT cycle number =     11
:
: function value    229.47993    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.18454401    
: Gamma decreased to   0.17703086    
:
:
: fvalues    0.0000000       229.47993       229.44974       229.47993    
:
:
:     CGMAT cycle number =     12
:
: function value    229.44974    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17703086    
: Gamma decreased to   0.17020072    
:
:
: fvalues    0.0000000       229.44974       229.42068       229.44974    
:
:
:     CGMAT cycle number =     13
:
: function value    229.42068    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17020072    
: Gamma decreased to   0.16399151    
:
:
: fvalues    0.0000000       229.42068       229.39333       229.42068    
:
:
:     CGMAT cycle number =     14
:
: function value    229.39333    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.16399151    
: Gamma decreased to   0.15834677    
:
:
: fvalues    0.0000000       229.39333       229.36681       229.39333    
:
:
:     CGMAT cycle number =     15
:
: function value    229.36681    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15834677    
: Gamma decreased to   0.15321518    
:
:
: fvalues    0.0000000       229.36681       229.34163       229.36681    
:
:
:     CGMAT cycle number =     16
:
: function value    229.34163    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15321518    
: Gamma decreased to   0.14855011    
:
:
: fvalues    0.0000000       229.34163       229.31769       229.34163    
:
:
:     CGMAT cycle number =     17
:
: function value    229.31769    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14855011    
: Gamma decreased to   0.14430913    
:
:
: fvalues    0.0000000       229.31769       229.29506       229.31769    
:
:
:     CGMAT cycle number =     18
:
: function value    229.29506    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14430913    
: Gamma decreased to   0.14045370    
:
:
: fvalues    0.0000000       229.29506       229.27348       229.29506    
:
:
:     CGMAT cycle number =     19
:
: function value    229.27348    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14045370    
: Gamma decreased to   0.13694876    
:
:
: fvalues    0.0000000       229.27348       229.25328       229.27348    
:
:
:     CGMAT cycle number =     20
:
: function value    229.25328    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13694876    
: Gamma decreased to   0.13376246    
:
:
: fvalues    0.0000000       229.25328       229.23459       229.25328    
:
:
:     CGMAT cycle number =      1
:
: function value    3954.6292    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     3.958     3.000
:Bond angles  : others                            26     1.410     3.000
:Torsion angles, period  1. refined               15     1.476    15.000
:Torsion angles, period  1. others                 3     0.190    15.000
:Torsion angles, period  3. refined                4     7.029    15.000
:Chiral centres: refined atoms                     4     0.035     0.200
:Planar groups: refined atoms                     14     0.002     0.020
:Planar groups: others                             6     0.000     0.020
:VDW repulsions.others                             1     0.000     0.200
:VDW; torsion: refined_atoms                       6     0.007     0.200
:VDW; torsion.others                               6     0.000     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       3954.6292       1645.5861       3954.6292    
:
:
:     CGMAT cycle number =      2
:
: function value    1645.5861    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.064     0.020
:Bond distances: others                           12     0.011     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       1645.5861       1504.8378       1645.5861    
:
:
:     CGMAT cycle number =      3
:
: function value    1504.8378    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.054     0.020
:Bond distances: others                           12     0.010     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       1504.8378       1416.2617       1504.8378    
:
:
:     CGMAT cycle number =      4
:
: function value    1416.2617    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.048     0.020
:Bond distances: others                           12     0.008     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Not converging with gamma equal   2.49090921E-02
: Trying gamma equal   7.03636408E-02
: Gamma decreased to   6.12727329E-02
:
:
: fvalues    0.0000000       1416.2617       1384.2695       1416.2617    
:
:
:     CGMAT cycle number =      5
:
: function value    1384.2695    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.045     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.12727329E-02
: Not converging with gamma equal   6.12727329E-02
: Trying gamma equal   0.10672728    
: Not converging with gamma equal   0.10672728    
: Trying gamma equal   0.15672728    
: Gamma decreased to   0.14672728    
:
:
: fvalues    0.0000000       1384.2695       1370.8711       1384.2695    
:
:
:     CGMAT cycle number =      6
:
: function value    1370.8711    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.045     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14672728    
: Gamma decreased to   0.13763636    
:
:
: fvalues    0.0000000       1370.8711       1358.0048       1370.8711    
:
:
:     CGMAT cycle number =      7
:
: function value    1358.0048    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.044     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13763636    
: Gamma decreased to   0.12937190    
:
:
: fvalues    0.0000000       1358.0048       1345.6464       1358.0048    
:
:
:     CGMAT cycle number =      8
:
: function value    1345.6464    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.043     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12937190    
: Gamma decreased to   0.12185875    
:
:
: fvalues    0.0000000       1345.6464       1333.7854       1345.6464    
:
:
:     CGMAT cycle number =      9
:
: function value    1333.7854    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.043     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12185875    
: Gamma decreased to   0.11502861    
:
:
: fvalues    0.0000000       1333.7854       1322.4045       1333.7854    
:
:
:     CGMAT cycle number =     10
:
: function value    1322.4045    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11502861    
: Gamma decreased to   0.10881940    
:
:
: fvalues    0.0000000       1322.4045       1311.4878       1322.4045    
:
:
:     CGMAT cycle number =     11
:
: function value    1311.4878    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.006     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10881940    
: Gamma decreased to   0.10317466    
:
:
: fvalues    0.0000000       1311.4878       1301.0240       1311.4878    
:
:
:     CGMAT cycle number =     12
:
: function value    1301.0240    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10317466    
: Gamma decreased to   9.80430841E-02
:
:
: fvalues    0.0000000       1301.0240       1290.9941       1301.0240    
:
:
:     CGMAT cycle number =     13
:
: function value    1290.9941    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.80430841E-02
: Not converging with gamma equal   9.80430841E-02
: Trying gamma equal   0.12370099    
: Gamma decreased to   0.11856941    
:
:
: fvalues    0.0000000       1290.9941       1283.1353       1290.9941    
:
:
:     CGMAT cycle number =     14
:
: function value    1283.1353    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11856941    
: Gamma decreased to   0.11390433    
:
:
: fvalues    0.0000000       1283.1353       1275.5366       1283.1353    
:
:
:     CGMAT cycle number =     15
:
: function value    1275.5366    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11390433    
: Gamma decreased to   0.10966336    
:
:
: fvalues    0.0000000       1275.5366       1268.1951       1275.5366    
:
:
:     CGMAT cycle number =     16
:
: function value    1268.1951    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10966336    
: Gamma decreased to   0.10580793    
:
:
: fvalues    0.0000000       1268.1951       1261.1099       1268.1951    
:
:
:     CGMAT cycle number =     17
:
: function value    1261.1099    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10580793    
: Gamma decreased to   0.10230299    
:
:
: fvalues    0.0000000       1261.1099       1254.2709       1261.1099    
:
:
:     CGMAT cycle number =     18
:
: function value    1254.2709    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.10230299    
: Gamma decreased to   9.91166830E-02
:
:
: fvalues    0.0000000       1254.2709       1247.6791       1254.2709    
:
:
:     CGMAT cycle number =     19
:
: function value    1247.6791    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.91166830E-02
: Gamma decreased to   9.62200388E-02
:
:
: fvalues    0.0000000       1247.6791       1241.3260       1247.6791    
:
:
:     CGMAT cycle number =     20
:
: function value    1241.3260    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.62200388E-02
: Gamma decreased to   9.35867280E-02
:
:
: fvalues    0.0000000       1241.3260       1235.2091       1241.3260    
:
:
:     CGMAT cycle number =      1
:
: function value    74.495377    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.039     0.020
:Bond distances: others                           12     0.004     0.020
:Bond angles  : refined atoms                     40     2.272     3.000
:Bond angles  : others                            26     0.421     3.000
:Torsion angles, period  1. refined               15     5.524    15.000
:Torsion angles, period  1. others                 3    15.708    15.000
:Torsion angles, period  3. refined                4    13.494    15.000
:Chiral centres: refined atoms                     4     0.106     0.200
:Planar groups: refined atoms                     14     0.010     0.020
:Planar groups: others                             6     0.001     0.020
:VDW repulsions.others                             4     0.054     0.200
:VDW; torsion: refined_atoms                       4     0.320     0.200
:VDW; torsion.others                               6     0.092     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
:
:
: fvalues    0.0000000       74.495377       28.820347       74.495377    
:
:
:     CGMAT cycle number =      2
:
: function value    28.820347    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.009     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
:
:
: fvalues    0.0000000       28.820347       26.893410       28.820347    
:
:
:     CGMAT cycle number =      3
:
: function value    26.893410    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
:
:
: fvalues    0.0000000       26.893410       26.455139       26.893410    
:
:
:     CGMAT cycle number =      4
:
: function value    26.455139    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.007     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Not converging with gamma equal   2.49090921E-02
: Trying gamma equal   7.03636408E-02
: Gamma decreased to   6.12727329E-02
:
:
: fvalues    0.0000000       26.455139       26.371088       26.455139    
:
:
:     CGMAT cycle number =      5
:
: function value    26.371088    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.12727329E-02
: Not converging with gamma equal   6.12727329E-02
: Trying gamma equal   0.10672728    
: Not converging with gamma equal   0.10672728    
: Trying gamma equal   0.15672728    
: Not converging with gamma equal   0.15672728    
: Trying gamma equal   0.21172729    
: Gamma decreased to   0.20072728    
:
:
: fvalues    0.0000000       26.371088       26.350555       26.371088    
:
:
:     CGMAT cycle number =      6
:
: function value    26.350555    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.20072728    
: Gamma decreased to   0.19072728    
:
:
: fvalues    0.0000000       26.350555       26.334232       26.350555    
:
:
:     CGMAT cycle number =      7
:
: function value    26.334232    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.19072728    
: Gamma decreased to   0.18163636    
:
:
: fvalues    0.0000000       26.334232       26.320751       26.334232    
:
:
:     CGMAT cycle number =      8
:
: function value    26.320751    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.18163636    
: Gamma decreased to   0.17337190    
:
:
: fvalues    0.0000000       26.320751       26.309345       26.320751    
:
:
:     CGMAT cycle number =      9
:
: function value    26.309345    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17337190    
: Gamma decreased to   0.16585875    
:
:
: fvalues    0.0000000       26.309345       26.299595       26.309345    
:
:
:     CGMAT cycle number =     10
:
: function value    26.299595    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.16585875    
: Gamma decreased to   0.15902860    
:
:
: fvalues    0.0000000       26.299595       26.291113       26.299595    
:
:
:     CGMAT cycle number =     11
:
: function value    26.291113    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15902860    
: Gamma decreased to   0.15281940    
:
:
: fvalues    0.0000000       26.291113       26.283710       26.291113    
:
:
:     CGMAT cycle number =     12
:
: function value    26.283710    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15281940    
: Gamma decreased to   0.14717466    
:
:
: fvalues    0.0000000       26.283710       26.277178       26.283710    
:
:
:     CGMAT cycle number =     13
:
: function value    26.277178    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14717466    
: Gamma decreased to   0.14204307    
:
:
: fvalues    0.0000000       26.277178       26.271406       26.277178    
:
:
:     CGMAT cycle number =     14
:
: function value    26.271406    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14204307    
: Gamma decreased to   0.13737799    
:
:
: fvalues    0.0000000       26.271406       26.266275       26.271406    
:
:
:     CGMAT cycle number =     15
:
: function value    26.266275    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13737799    
: Gamma decreased to   0.13313702    
:
:
: fvalues    0.0000000       26.266275       26.261736       26.266275    
:
:
:     CGMAT cycle number =     16
:
: function value    26.261736    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.13313702    
: Gamma decreased to   0.12928158    
:
:
: fvalues    0.0000000       26.261736       26.257744       26.261736    
:
:
:     CGMAT cycle number =     17
:
: function value    26.257744    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12928158    
: Gamma decreased to   0.12577665    
:
:
: fvalues    0.0000000       26.257744       26.254160       26.257744    
:
:
:     CGMAT cycle number =     18
:
: function value    26.254160    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12577665    
: Gamma decreased to   0.12259034    
:
:
: fvalues    0.0000000       26.254160       26.250973       26.254160    
:
:
:     CGMAT cycle number =     19
:
: function value    26.250973    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.12259034    
: Gamma decreased to   0.11969370    
:
:
: fvalues    0.0000000       26.250973       26.248142       26.250973    
:
:
:     CGMAT cycle number =     20
:
: function value    26.248142    
:
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.006     0.020
:Bond distances: others                           12     0.000     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.11969370    
: Gamma decreased to   0.11706039    
:
:
: fvalues    0.0000000       26.248142       26.245613       26.248142    
:  Time in seconds: CPU =         0.48
:             Elapsed =           0.00
:
:    ****           Things for loggraph, R factor and others vs cycle            ****
:
:
:$TABLE: Rfactor analysis, stats vs cycle  :
:$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
::FOM vs cycle :N:1,4:
::-LL vs cycle :N:1,5:
::-LLfree vs cycle :N:1,6:
::Geometry vs cycle:N:1,7,8,9,10,11:
:$$
:    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
:$$
:       0   0.0      0.0      0.0           0.       0.0   0.0304  1.521   4.292  1.431   0.186
:       1   0.0      0.0      0.0           0.       0.0   0.0813  4.066   4.676  1.559   0.043
:       2   0.0      0.0      0.0           0.       0.0   0.0794  3.972   4.318  1.439   0.037
:       3   0.0      0.0      0.0           0.       0.0   0.0760  3.798   4.058  1.353   0.017
:       4   0.0      0.0      0.0           0.       0.0   0.0754  3.772   4.010  1.337   0.026
:       5   0.0      0.0      0.0           0.       0.0   0.0754  3.772   3.985  1.328   0.037
:       6   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.981  1.327   0.036
:       7   0.0      0.0      0.0           0.       0.0   0.0754  3.771   3.978  1.326   0.036
:       8   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.969  1.323   0.035
:       9   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.965  1.322   0.035
:      10   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      11   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.964  1.321   0.035
:      12   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      13   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.963  1.321   0.035
:      14   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.962  1.321   0.035
:      15   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      16   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.961  1.320   0.035
:      17   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      18   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.960  1.320   0.035
:      19   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.959  1.320   0.035
:      20   0.0      0.0      0.0           0.       0.0   0.0754  3.770   3.958  1.319   0.035
:      21   0.0      0.0      0.0           0.       0.0   0.0637  3.184   2.578  0.859   0.088
:      22   0.0      0.0      0.0           0.       0.0   0.0539  2.697   2.487  0.829   0.085
:      23   0.0      0.0      0.0           0.       0.0   0.0477  2.384   2.425  0.808   0.093
:      24   0.0      0.0      0.0           0.       0.0   0.0455  2.273   2.401  0.800   0.098
:      25   0.0      0.0      0.0           0.       0.0   0.0446  2.229   2.391  0.797   0.100
:      26   0.0      0.0      0.0           0.       0.0   0.0438  2.191   2.380  0.793   0.101
:      27   0.0      0.0      0.0           0.       0.0   0.0432  2.158   2.370  0.790   0.102
:      28   0.0      0.0      0.0           0.       0.0   0.0426  2.128   2.360  0.787   0.103
:      29   0.0      0.0      0.0           0.       0.0   0.0420  2.102   2.351  0.784   0.104
:      30   0.0      0.0      0.0           0.       0.0   0.0416  2.079   2.341  0.780   0.105
:      31   0.0      0.0      0.0           0.       0.0   0.0412  2.058   2.332  0.777   0.106
:      32   0.0      0.0      0.0           0.       0.0   0.0408  2.040   2.323  0.774   0.106
:      33   0.0      0.0      0.0           0.       0.0   0.0405  2.026   2.316  0.772   0.107
:      34   0.0      0.0      0.0           0.       0.0   0.0403  2.013   2.309  0.770   0.107
:      35   0.0      0.0      0.0           0.       0.0   0.0400  2.000   2.302  0.767   0.107
:      36   0.0      0.0      0.0           0.       0.0   0.0398  1.989   2.296  0.765   0.107
:      37   0.0      0.0      0.0           0.       0.0   0.0396  1.978   2.290  0.763   0.107
:      38   0.0      0.0      0.0           0.       0.0   0.0394  1.968   2.283  0.761   0.107
:      39   0.0      0.0      0.0           0.       0.0   0.0392  1.958   2.277  0.759   0.106
:      40   0.0      0.0      0.0           0.       0.0   0.0390  1.949   2.272  0.757   0.106
:      41   0.0      0.0      0.0           0.       0.0   0.0087  0.435   2.793  0.931   0.046
:      42   0.0      0.0      0.0           0.       0.0   0.0070  0.349   2.801  0.934   0.036
:      43   0.0      0.0      0.0           0.       0.0   0.0065  0.327   2.808  0.936   0.034
:      44   0.0      0.0      0.0           0.       0.0   0.0065  0.324   2.810  0.937   0.034
:      45   0.0      0.0      0.0           0.       0.0   0.0065  0.323   2.810  0.937   0.034
:      46   0.0      0.0      0.0           0.       0.0   0.0064  0.322   2.810  0.937   0.034
:      47   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.810  0.937   0.034
:      48   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.810  0.937   0.034
:      49Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 96 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "3GP"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/3/3GP.cif
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:44:53_2013_modification_0.pdb.gz
There are 2 data in coot-ccp4/libcheck_3GP.cif
Welcome to Coot
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:44:53_2013_modification_1.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/monomer-3GP.pdb
 PDB file /home/emsley/data/greg-data/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 97 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb
 PDB file /home/emsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 98 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 
Reading coordinate file: /home/emsley/data/greg-data/test-LIG.pdb
 PDB file /home/emsley/data/greg-data/test-LIG.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 99 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "LIG"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIG.cif
INFO:: comp-id: LIG is marked for non-autoloading - stopping now 
INFO:: backup file coot-backup/coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:44:53_2013_modification_2.pdb.gz
No graphics!  Can't make Map Selection dialog.
------------ ERROR! -------------------
       moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
attempting to delete NULL moving_atoms_asc.mol
ignoring 
Reading coordinate file: /home/emsley/data/greg-data/monomer-NPO.pdb
 PDB file /home/emsley/data/greg-data/monomer-NPO.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 100 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
Reading coordinate file: /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb
 PDB file /home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 107/113
INFO:: NCS chain comparison 10/113
INFO:: NCS chain comparison 0/113
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 10/117
INFO:: NCS chain comparison 112/117
INFO:: NCS chain comparison 0/117
  INFO:: fill_ghost_info Constructed 6 ghosts
      Ghost 0 name: "NCS found from matching Chain C onto Chain A"
      Ghost 1 name: "NCS found from matching Chain E onto Chain A"
      Ghost 2 name: "NCS found from matching Chain G onto Chain A"
      Ghost 3 name: "NCS found from matching Chain D onto Chain B"
      Ghost 4 name: "NCS found from matching Chain F onto Chain B"
      Ghost 5 name: "NCS found from matching Chain H onto Chain B"
Molecule 106 read successfully
DEBUG:: there were 0 types with no dictionary 
making conventional map from MTZ filename /home/emsley/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:: 0.136 seconds to read MTZ file
INFO:: 0.098 seconds to initialize map
INFO:: 0.071 seconds for FFT
INFO:: 0.007 seconds for statistics
      Map mean: ........ -8.79008e-07
      Map sigma: ....... 0.171188
      Map maximum: ..... 1.34304
      Map minimum: ..... -0.695441
INFO:: 0.008 seconds for contour map
INFO:: 0.32 seconds in total
making difference map from MTZ filename /home/emsley/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:: 0.078 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.071 seconds for FFT
INFO:: 0.006 seconds for statistics
      Map mean: ........ 2.09389e-06
      Map sigma: ....... 0.0333923
      Map maximum: ..... 0.366077
      Map minimum: ..... -0.191665
INFO:: 0.003 seconds for contour map
INFO:: 0.159 seconds in total
Executing ligand search...
INFO:: ligand number 0 is molecule number 100   with wiggly flag: 0
Protein centre at: xyz = (     58.29,     34.65,     30.63)
Map statistics: mean: -0.0216745 st.d: 0.0886263
Map statistics: min: -0.695441, max: 0.754209
-0.659199    14
-0.586717    143
-0.514234    1331
-0.441752    5299
-0.369269    11732
-0.296787    16725
-0.224304    21484
-0.151822    46755
-0.0793394    161104
-0.00685694    614773
0.0656256    162933
0.138108    28508
0.210591    3055
0.283073    813
0.355556    334
0.428038    197
0.500521    78
0.573003    48
0.645486    25
0.717968    9
0.790451    0
INFO:: find_clusters map_rms is 0.171132
INFO:: Using density cut-off: 0.171132 (1 sigma)  (mean -0.0216776 stdev: 0.0886191)
INFO:: Using water to protein distance limits: 2.4 3.2
Finding clusters...done
debug:: n_ligands_for_cluster() top_score 4.04309 and 4 are decent out of 12
score_and_resort_using_correlation iclust: 0 n_ligs 12 n_sol 4
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.710467
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.650554
----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.597263
----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.60981
------------------ 12 solutions for cluster 0 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 4.04309 r-state: [1 correl-score 0.710467] (atom-score: 0.404309) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 4.02776 r-state: [1 correl-score 0.650554] (atom-score: 0.402776) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 3.8627 r-state: [1 correl-score 0.60981] (atom-score: 0.38627) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 3.8769 r-state: [1 correl-score 0.597263] (atom-score: 0.38769) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 2.37512 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 2.37158 r-state: [0] (atom-score: 0.237158) many-atoms-fit: 1 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 2.06071 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.95875 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 0.649721 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.619694 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.582693 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.49419 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 2 [ligand-score: #0 at-score: 4.04309 r-state: [1 correl-score 0.710467] (atom-score: 0.404309) many-atoms-fit: 1 n-atoms: 10]
limit solutions: 1 of 2 [ligand-score: #0 at-score: 4.02776 r-state: [1 correl-score 0.650554] (atom-score: 0.402776) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.01651 and 4 are decent out of 12
score_and_resort_using_correlation iclust: 1 n_ligs 12 n_sol 4
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.676577
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.688904
----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.56899
----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.554978
------------------ 12 solutions for cluster 1 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 1.99864 r-state: [1 correl-score 0.688904] (atom-score: 0.199864) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 2.01651 r-state: [1 correl-score 0.676577] (atom-score: 0.201651) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.91517 r-state: [1 correl-score 0.56899] (atom-score: 0.191517) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.85929 r-state: [1 correl-score 0.554978] (atom-score: 0.185929) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.54282 r-state: [0] (atom-score: 0.154282) many-atoms-fit: 1 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.53711 r-state: [0] (atom-score: 0.153711) many-atoms-fit: 1 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.52571 r-state: [0] (atom-score: 0.152571) many-atoms-fit: 1 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.51104 r-state: [0] (atom-score: 0.151104) many-atoms-fit: 1 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 1.2013 r-state: [0] (atom-score: 0.12013) many-atoms-fit: 1 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 1.17002 r-state: [0] (atom-score: 0.117002) many-atoms-fit: 1 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 1.11377 r-state: [0] (atom-score: 0.111377) many-atoms-fit: 1 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 1.11225 r-state: [0] (atom-score: 0.111225) many-atoms-fit: 1 n-atoms: 10]
limit solutions: 0 of 2 [ligand-score: #0 at-score: 1.99864 r-state: [1 correl-score 0.688904] (atom-score: 0.199864) many-atoms-fit: 1 n-atoms: 10]
limit solutions: 1 of 2 [ligand-score: #0 at-score: 2.01651 r-state: [1 correl-score 0.676577] (atom-score: 0.201651) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.08817 and 4 are decent out of 12
score_and_resort_using_correlation iclust: 2 n_ligs 12 n_sol 4
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.61907
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.641407
----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.630588
----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.572928
------------------ 12 solutions for cluster 2 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 2.0869 r-state: [1 correl-score 0.641407] (atom-score: 0.20869) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 2.04526 r-state: [1 correl-score 0.630588] (atom-score: 0.204526) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 2.08817 r-state: [1 correl-score 0.61907] (atom-score: 0.208817) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 2.01631 r-state: [1 correl-score 0.572928] (atom-score: 0.201631) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.25358 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.25343 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.19404 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.15181 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 0.734044 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.702536 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.609291 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.601228 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 3 [ligand-score: #0 at-score: 2.0869 r-state: [1 correl-score 0.641407] (atom-score: 0.20869) many-atoms-fit: 1 n-atoms: 10]
limit solutions: 1 of 3 [ligand-score: #0 at-score: 2.04526 r-state: [1 correl-score 0.630588] (atom-score: 0.204526) many-atoms-fit: 1 n-atoms: 10]
limit solutions: 2 of 3 [ligand-score: #0 at-score: 2.08817 r-state: [1 correl-score 0.61907] (atom-score: 0.208817) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
Symmetry available for this molecule
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.85941 and 3 are decent out of 12
score_and_resort_using_correlation iclust: 3 n_ligs 12 n_sol 3
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.21745
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.0817361
----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.115202
------------------ 12 solutions for cluster 3 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 1.85941 r-state: [1 correl-score 0.21745] (atom-score: 0.185941) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 1.76094 r-state: [1 correl-score 0.115202] (atom-score: 0.176094) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.80685 r-state: [1 correl-score 0.0817361] (atom-score: 0.180685) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.55964 r-state: [0] (atom-score: 0.155964) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.53921 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.53817 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.1206 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.11385 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 0.825835 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.817365 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.815745 r-state: [0] (atom-score: 0.0815745) many-atoms-fit: 1 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.741973 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.85941 r-state: [1 correl-score 0.21745] (atom-score: 0.185941) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.38901 and 3 are decent out of 12
score_and_resort_using_correlation iclust: 4 n_ligs 12 n_sol 3
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation -0.0447292
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.023702
----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.213383
------------------ 12 solutions for cluster 4 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 1.27054 r-state: [1 correl-score 0.213383] (atom-score: 0.127054) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 1.3219 r-state: [1 correl-score 0.023702] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.38901 r-state: [1 correl-score -0.0447292] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.23707 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.17936 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.15652 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.1559 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.15145 r-state: [0] (atom-score: 0.115145) many-atoms-fit: 1 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 1.0791 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 1.05142 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.951901 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.897714 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.27054 r-state: [1 correl-score 0.213383] (atom-score: 0.127054) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.62329 and 4 are decent out of 12
score_and_resort_using_correlation iclust: 5 n_ligs 12 n_sol 4
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.172844
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.182423
----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.215354
----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.18106
------------------ 12 solutions for cluster 5 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 1.49289 r-state: [1 correl-score 0.215354] (atom-score: 0.149289) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 1.62089 r-state: [1 correl-score 0.182423] (atom-score: 0.162089) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.47803 r-state: [1 correl-score 0.18106] (atom-score: 0.147803) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.62329 r-state: [1 correl-score 0.172844] (atom-score: 0.162329) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.42128 r-state: [0] (atom-score: 0.142128) many-atoms-fit: 1 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.41456 r-state: [0] (atom-score: 0.141456) many-atoms-fit: 1 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.41066 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.3787 r-state: [0] (atom-score: 0.13787) many-atoms-fit: 1 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 0.97905 r-state: [0] (atom-score: 0.097905) many-atoms-fit: 1 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.855389 r-state: [0] (atom-score: 0.0855389) many-atoms-fit: 1 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.835225 r-state: [0] (atom-score: 0.0835225) many-atoms-fit: 1 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.755734 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.49289 r-state: [1 correl-score 0.215354] (atom-score: 0.149289) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.07828 and 2 are decent out of 12
score_and_resort_using_correlation iclust: 6 n_ligs 12 n_sol 2
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.185659
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.141778
------------------ 12 solutions for cluster 6 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 2.07828 r-state: [1 correl-score 0.185659] (atom-score: 0.207828) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 2.03408 r-state: [1 correl-score 0.141778] (atom-score: 0.203408) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.68755 r-state: [0] (atom-score: 0.168755) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.63335 r-state: [0] (atom-score: 0.163335) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.61106 r-state: [0] (atom-score: 0.161106) many-atoms-fit: 1 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.61013 r-state: [0] (atom-score: 0.161013) many-atoms-fit: 1 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.59877 r-state: [0] (atom-score: 0.159877) many-atoms-fit: 1 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.53303 r-state: [0] (atom-score: 0.153303) many-atoms-fit: 1 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 0.942882 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.942428 r-state: [0] (atom-score: 0.0942428) many-atoms-fit: 1 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.909942 r-state: [0] (atom-score: 0.0909942) many-atoms-fit: 1 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.796521 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 1 [ligand-score: #0 at-score: 2.07828 r-state: [1 correl-score 0.185659] (atom-score: 0.207828) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.60922 and 2 are decent out of 12
score_and_resort_using_correlation iclust: 7 n_ligs 12 n_sol 2
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.224766
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.0535896
------------------ 12 solutions for cluster 7 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 1.60922 r-state: [1 correl-score 0.224766] (atom-score: 0.160922) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 1.50926 r-state: [1 correl-score 0.0535896] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.39653 r-state: [0] (atom-score: 0.139653) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.35384 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.3487 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.189 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.17364 r-state: [0] (atom-score: 0.117364) many-atoms-fit: 1 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.10348 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 1.03613 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.982172 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.961542 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.867246 r-state: [0] (atom-score: 0.0867246) many-atoms-fit: 1 n-atoms: 10]
limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.60922 r-state: [1 correl-score 0.224766] (atom-score: 0.160922) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 2.10846 and 2 are decent out of 12
score_and_resort_using_correlation iclust: 8 n_ligs 12 n_sol 2
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.159373
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.252585
------------------ 12 solutions for cluster 8 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 1.99177 r-state: [1 correl-score 0.252585] (atom-score: 0.199177) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 2.10846 r-state: [1 correl-score 0.159373] (atom-score: 0.210846) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.47607 r-state: [0] (atom-score: 0.147607) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.41627 r-state: [0] (atom-score: 0.141627) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.40709 r-state: [0] (atom-score: 0.140709) many-atoms-fit: 1 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.27072 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.20091 r-state: [0] (atom-score: 0.120091) many-atoms-fit: 1 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.19269 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 0.921284 r-state: [0] (atom-score: 0.0921284) many-atoms-fit: 1 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.891549 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.728988 r-state: [0] (atom-score: 0.0728988) many-atoms-fit: 1 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.683474 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 1 [ligand-score: #0 at-score: 1.99177 r-state: [1 correl-score 0.252585] (atom-score: 0.199177) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
debug:: n_ligands_for_cluster() top_score 1.81356 and 4 are decent out of 12
score_and_resort_using_correlation iclust: 9 n_ligs 12 n_sol 4
----- in get_correl() constructed spec for i 0 [spec: MinInt4 "A" 1 ""] which has correlation 0.276934
----- in get_correl() constructed spec for i 1 [spec: MinInt4 "A" 1 ""] which has correlation 0.376081
----- in get_correl() constructed spec for i 2 [spec: MinInt4 "A" 1 ""] which has correlation 0.417633
----- in get_correl() constructed spec for i 3 [spec: MinInt4 "A" 1 ""] which has correlation 0.279897
------------------ 12 solutions for cluster 9 ------------- 
post correl 0 of 12 [ligand-score: #0 at-score: 1.74019 r-state: [1 correl-score 0.417633] (atom-score: 0.174019) many-atoms-fit: 1 n-atoms: 10]
post correl 1 of 12 [ligand-score: #0 at-score: 1.77141 r-state: [1 correl-score 0.376081] (atom-score: 0.177141) many-atoms-fit: 1 n-atoms: 10]
post correl 2 of 12 [ligand-score: #0 at-score: 1.73205 r-state: [1 correl-score 0.279897] (atom-score: 0.173205) many-atoms-fit: 1 n-atoms: 10]
post correl 3 of 12 [ligand-score: #0 at-score: 1.81356 r-state: [1 correl-score 0.276934] (atom-score: 0.181356) many-atoms-fit: 1 n-atoms: 10]
post correl 4 of 12 [ligand-score: #0 at-score: 1.2024 r-state: [0] (atom-score: 0.12024) many-atoms-fit: 1 n-atoms: 10]
post correl 5 of 12 [ligand-score: #0 at-score: 1.17738 r-state: [0] (atom-score: 0.117738) many-atoms-fit: 1 n-atoms: 10]
post correl 6 of 12 [ligand-score: #0 at-score: 1.06634 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 7 of 12 [ligand-score: #0 at-score: 1.06434 r-state: [0] (atom-score: 0.106434) many-atoms-fit: 1 n-atoms: 10]
post correl 8 of 12 [ligand-score: #0 at-score: 0.607552 r-state: [0] (atom-score: 0.0607552) many-atoms-fit: 1 n-atoms: 10]
post correl 9 of 12 [ligand-score: #0 at-score: 0.467374 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 10 of 12 [ligand-score: #0 at-score: 0.426473 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
post correl 11 of 12 [ligand-score: #0 at-score: 0.370657 r-state: [0] (atom-score: 0) many-atoms-fit: 0 n-atoms: 10]
limit solutions: 0 of 2 [ligand-score: #0 at-score: 1.74019 r-state: [1 correl-score 0.417633] (atom-score: 0.174019) many-atoms-fit: 1 n-atoms: 10]
limit solutions: 1 of 2 [ligand-score: #0 at-score: 1.77141 r-state: [1 correl-score 0.376081] (atom-score: 0.177141) many-atoms-fit: 1 n-atoms: 10]
Symmetry available for this molecule
Symmetry available for this molecule
Reading coordinate file: coot-ccp4/monomer-3GP.pdb
 PDB file coot-ccp4/monomer-3GP.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 125 read successfully
DEBUG:: there were 0 types with no dictionary 
Symmetry available for this molecule
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:45:04_2013_modification_0.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:45:04_2013_modification_1.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:45:04_2013_modification_2.pdb.gz
INFO:: replace_coords: 36 atoms updated.
INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Fri_Sep_13_04:45:04_2013_modification_3.pdb.gz
INFO:: replace_coords: 36 atoms updated.
Reading coordinate file: /home/emsley/data/greg-data/dipole-residues.pdb
 PDB file /home/emsley/data/greg-data/dipole-residues.pdb has been read.
No Spacegroup found for this PDB file
INFO:: Found 1 models
   Model 1 had 0 links
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
Molecule 127 read successfully
DEBUG:: there were 0 types with no dictionary 
WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
WARNING: in init_refmac_mon_lib file "/home/emsley/data/greg-data/libcheck_3GP.cif" not found.
init_refmac_mon_lib /home/emsley/data/greg-data/libcheck_3GP.cif had no bond restraints
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 128 read successfully
DEBUG:: there were 0 types with no dictionary 
storing sequence: ACDEFGHIKLMNPQ for chain id: A in molecule number 128
storing sequence: ACDEFGHIKLMNPQRST for chain id: A in molecule number 128
Reading coordinate file: /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb
 PDB file /home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 1/2
INFO:: NCS chain comparison 0/2
INFO:: NCS chain comparison 0/13
Molecule 129 read successfully
DEBUG:: there were 0 types with no dictionary 
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.025 seconds to read MTZ file
INFO:: 0.001 seconds to initialize map
INFO:: 0.015 seconds for FFT
INFO:: 0.001 seconds for statistics
      Map mean: ........ 1.06932e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.019 seconds for contour map
INFO:: 0.061 seconds in total
storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A in molecule number 129

Sequence: ?EYTVITPGARTR
Confidence: 0.999999

From    : HEYTVITPGARTR
Chain id: 0	Offset: 53
INFO:: backup file coot-backup/_home_emsley_data_greg-data_crashes_on_cootaneering-v2.pdb_Fri_Sep_13_04:45:07_2013_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.
INFO:: 5 matched atoms had: 
   mean devi: 0
    rms devi: 0
    max devi: 0
    min devi: 0
INFO:: 5 matched atoms had: 
   mean devi: 0.0120681
    rms devi: 0.0134464
    max devi: 0.0214179
    min devi: 0.00385596
INFO:: 5 matched atoms had: 
   mean devi: 0.270216
    rms devi: 0.335002
    max devi: 0.536002
    min devi: 0.08463
INFO:: 5 matched atoms had: 
   mean devi: 0.26738
    rms devi: 0.322791
    max devi: 0.495136
    min devi: 0.112289
INFO:: 5 matched atoms had: 
   mean devi: 0.270247
    rms devi: 0.335033
    max devi: 0.536044
    min devi: 0.0847029
INFO:: 5 matched atoms had: 
   mean devi: 0.267411
    rms devi: 0.322823
    max devi: 0.495177
    min devi: 0.112221
INFO:: 5 matched atoms had: 
   mean devi: 0.011982
    rms devi: 0.013349
    max devi: 0.0212578
    min devi: 0.0038732
INFO:: 5 matched atoms had: 
   mean devi: 0.000242576
    rms devi: 0.000242751
    max devi: 0.000256671
    min devi: 0.000231275
INFO:: 5 matched atoms had: 
   mean devi: 0.270185
    rms devi: 0.334971
    max devi: 0.535961
    min devi: 0.0845571
INFO:: 5 matched atoms had: 
   mean devi: 0.267349
    rms devi: 0.322759
    max devi: 0.495094
    min devi: 0.112357
INFO:: 5 matched atoms had: 
   mean devi: 6.9313e-05
    rms devi: 6.93629e-05
    max devi: 7.33402e-05
    min devi: 6.60841e-05
INFO:: 5 matched atoms had: 
   mean devi: 0.0120334
    rms devi: 0.0134072
    max devi: 0.0213538
    min devi: 0.00386188
INFO:: 5 matched atoms had: 
   mean devi: 0.000138622
    rms devi: 0.000138721
    max devi: 0.000146676
    min devi: 0.000132164
INFO:: 5 matched atoms had: 
   mean devi: 0.011999
    rms devi: 0.0133684
    max devi: 0.0212898
    min devi: 0.0038691
INFO:: 5 matched atoms had: 
   mean devi: 0.267426
    rms devi: 0.322839
    max devi: 0.495197
    min devi: 0.112187
INFO:: 5 matched atoms had: 
   mean devi: 0.270294
    rms devi: 0.335079
    max devi: 0.536106
    min devi: 0.0848122
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: backup file coot-backup/Ideal-A-form-RNA_Fri_Sep_13_04:45:07_2013_modification_0.pdb.gz
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
!! Warning:: No symmetry available for this molecule
No Symmetry for this model
INFO:: Matching/moving molecule number 133 to 133
ERROR:: No symmetry available
INFO:: LSQ matched 125 atoms
INFO:: 125 matched atoms had: 
   mean devi: 0.141862
    rms devi: 0.1486
    max devi: 0.243105
    min devi: 0.0283178
INFO:: Axis orientation: (    0.3864,   -0.6781,   -0.6252)
INFO:: Rotation in CCP4 Polar Angles: Polar = (128.694,-60.3228,0.295209)
INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Fri_Sep_13_04:45:08_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|         1,  0.003218, -0.003497|
| -0.003225,         1, -0.001985|
|  0.003491,  0.001997,         1|
(    -24.05,     -23.7,    -24.44)
No unit cell for this molecule, hence no fractional matrix.
Reading coordinate file: /home/emsley/data/greg-data/1wly.pdb
 PDB file /home/emsley/data/greg-data/1wly.pdb has been read.
Spacegroup: C 1 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 134 read successfully
DEBUG:: there were 0 types with no dictionary 
Reading coordinate file: /home/emsley/data/greg-data/1yb5.pdb
 PDB file /home/emsley/data/greg-data/1yb5.pdb has been read.
Spacegroup: P 21 21 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 324/324
INFO:: NCS chain comparison 0/324
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 135 read successfully
DEBUG:: there were 2 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "CL"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CL.cif
INFO:: using standard CCP4 Refmac dictionary to search for "NAP"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/n/NAP.cif
INFO:: reference 134 has 750 atoms selected
INFO:: moving    135 has 842 atoms selected
superposing...
number of Ca atoms in selections: 110 (moving) and 100 (reference)
Another Go...

      Moving  Reference   Distance
      A 6
      A 7
      A 8 <---> A 2  : 0.751   A
      A 9 <---> A 3  : 0.942174   A
      A 10 <---> A 4  : 0.629981   A
      A 11 <---> A 5  : 0.711865   A
      A 12 <---> A 6  : 0.631005   A
      A 13 <---> A 7  : 0.467533   A
      A 14 <---> A 8  : 0.426381   A
      A 15 <---> A 9  : 0.97919   A
      A 16 <---> A 10  : 0.754876   A
      A 17 <---> A 11  : 0.488388   A
      A 18 <---> A 12  : 0.745058   A
      A 19 <---> A 13  : 0.460612   A
      A 20 <---> A 14  : 1.2809   A
      A 21 <---> A 15  : 1.24119   A
      A 22 <---> A 16  : 1.07334   A
      A 23 <---> A 17  : 0.973042   A
      A 24 <---> A 18  : 0.470509   A
      A 25 <---> A 19  : 0.355977   A
      A 26 <---> A 20  : 3.11453   A
      A 27
      A 28 <---> A 21  : 1.57537   A
      A 29 <---> A 22  : 1.63223   A
      A 30
      A 31 <---> A 23  : 1.9973   A
      A 32 <---> A 25  : 1.83236   A
      A 33 <---> A 26  : 0.930954   A
      A 34 <---> A 27  : 0.680752   A
      A 35 <---> A 28  : 0.267434   A
      A 36 <---> A 29  : 0.599491   A
      A 37 <---> A 30  : 0.699234   A
      A 38 <---> A 31  : 0.862022   A
      A 39 <---> A 32  : 0.842095   A
      A 40 <---> A 33  : 0.720834   A
      A 41 <---> A 34  : 0.86807   A
      A 42 <---> A 35  : 0.778132   A
      A 43 <---> A 36  : 0.621112   A
      A 44 <---> A 37  : 0.465701   A
      A 45 <---> A 38  : 0.747499   A
      A 46 <---> A 39  : 0.517002   A
      A 47 <---> A 40  : 0.505788   A
      A 48 <---> A 41  : 0.889736   A
      A 49 <---> A 42  : 0.583476   A
      A 50 <---> A 43  : 0.434661   A
      A 51 <---> A 44  : 0.619207   A
      A 52 <---> A 45  : 0.215003   A
      A 53 <---> A 46  : 0.747368   A
      A 54 <---> A 47  : 1.02135   A
      A 55 <---> A 48  : 0.920754   A
      A 56 <---> A 49  : 0.939245   A
      A 57
      A 58
      A 59
      A 60
      A 61
      A 62
      A 63
      A 64
      A 65 <---> A 60  : 0.466577   A
      A 66 <---> A 61  : 0.0522595   A
      A 67 <---> A 62  : 1.07191   A
      A 68 <---> A 63  : 0.793315   A
      A 69 <---> A 64  : 0.891607   A
      A 70 <---> A 65  : 1.25797   A
      A 71 <---> A 66  : 0.693217   A
      A 72 <---> A 67  : 1.03452   A
      A 73 <---> A 68  : 1.44168   A
      A 74 <---> A 69  : 0.909171   A
      A 75 <---> A 70  : 1.61656   A
      A 76 <---> A 71  : 0.87415   A
      A 77 <---> A 72  : 0.238771   A
      A 78 <---> A 73  : 0.311753   A
      A 79 <---> A 74  : 0.388701   A
      A 80 <---> A 75  : 0.761327   A
      A 81 <---> A 76  : 0.904406   A
      A 82 <---> A 77  : 0.609012   A
      A 83 <---> A 78  : 1.79778   A
      A 84 <---> A 79  : 1.92564   A
      A 85 <---> A 80  : 1.34157   A
      A 86 <---> A 81  : 0.565753   A
      A 87 <---> A 82  : 0.448017   A
      A 88 <---> A 83  : 0.90782   A
      A 89 <---> A 84  : 0.362515   A
      A 90 <---> A 85  : 0.404031   A
      A 91 <---> A 86  : 0.458593   A
      A 92 <---> A 87  : 0.434035   A
      A 93 <---> A 88  : 0.366361   A
      A 94 <---> A 89  : 0.492061   A
      A 95 <---> A 90  : 0.649822   A
      A 96 <---> A 91  : 1.58048   A
      A 97 <---> A 92  : 2.88385   A
      A 98
      A 99
      A 100

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

 Moving: VIEAVGDNASAFKKGDRVFTSSTISGGYAEYALAADHTVY
 Target: VVEEVGPGVTDFTVGERVCTCL---GAYSQERLYPAEKLI

INFO:: backup file coot-backup/_home_emsley_data_greg-data_1yb5.pdb_Fri_Sep_13_04:45:09_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal 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 101.022 169.739
  Rotation - euler (alpha,beta,gamma) 40.0716 168.257 18.0277
  Translation - Angstroms             70.6538 7.793 21.2852 
INFO: core rmsd achieved: 1.01989 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
      sequence identity:           30.5263%
Error reading /home/emsley/data/greg-data/1pyd.pdb
   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.809  0.936   0.034
:      50   0.0      0.0      0.0           0.       0.0   0.0064  0.321   2.809  0.936   0.034
:      51   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      52   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      53   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.808  0.936   0.034
:      54   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      55   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      56   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.807  0.936   0.034
:      57   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
:      58   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
:      59   0.0      0.0      0.0           0.       0.0   0.0064  0.320   2.806  0.935   0.034
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
: Refmac_5.7.0029:  End of Refmac_5.7.0029 
:Times: User:       8.1s System:    0.4s Elapsed:     0:08  
:</pre>
:</html>
:<!--SUMMARY_END--></FONT></B>
INFO:: libcheck-minimal? is #f
PASS: Get monomer test
Entered testcase - Set Bond thickness
PASS: Set Bond thickness
Entered testcase - Delete all-molecule Hydrogens
here 1 
PASS: Delete all-molecule Hydrogens
Entered testcase - Non-Autoloads
PASS: Non-Autoloads
Entered testcase - Move and Refine Ligand test
PASS: Move and Refine Ligand test
Entered testcase - Many Molecules - Ligand Fitting
   Fitting NPO gave these results: (110 111 112 113 114 115 116 117 118 119 120 121 122 123 124)
PASS: Many Molecules - Ligand Fitting
Entered testcase - flip residue (around eigen vectors)
distance: 4.35071918939919
distance d2: 1.19209289550781e-7
PASS: flip residue (around eigen vectors)
Entered testcase - Test dipole
info:: dipole components (-2.21999993920326 4.44089209850063e-16 0.0) 
PASS: Test dipole
Entered testcase - Reading new dictionary restraints replaces
PASS: Reading new dictionary restraints replaces
Ended 03-ligand.scm
Running 04-cootaneer.scm ...
Entered testcase - Assignment of new PIR sequence overwrites old assignment
debug seq: ("A" . "ACDEFGHIKLMNPQ")
PASS: Assignment of new PIR sequence overwrites old assignment
Entered testcase - Cootaneer Beta Strand
   Cootaneering: imol 129 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf ""
PASS: Cootaneer Beta Strand
Ended 04-cootaneer.scm
Running 05-rna-ghosts.scm ...
Entered testcase - RNA NCS Ghosts
   There are 8 residues in chain "A"
   There are 8 residues in chain "B"
PASS: RNA NCS Ghosts
Ended 05-rna-ghosts.scm
Running 06-ssm.scm ...
Entered testcase - SSM - Frank von Delft's Example
PASS: SSM - Frank von Delft's Example
Entered testcase - SSM - Alice Dawson's Example
    0    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    2    "/home/emsley/data/greg-data/ins-code-fragment-pre.pdb"
    3    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    4    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    5    "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
    6    "test-3hfl.map"
    7    "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb"
    8    "atom selection from tutorial-add-terminal-1-test.pdb"
    9    "/home/emsley/data/greg-data/frag-2wot.pdb"
    10    "sphere selection from tutorial-modern.pdb"
    12    "/home/emsley/data/greg-data/rotamer-test-fragment.pdb"
    13    "/home/emsley/data/greg-data/res098.pdb"
    14    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    15    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    16    "/home/emsley/data/greg-data/pdb3knw.ent"
    19    "/home/emsley/data/greg-data/alt-conf-pepflip-test.pdb"
    20    "/home/emsley/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb"
    21    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    22    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    23    "/home/emsley/data/greg-data/tutorial-add-terminal-1-test.pdb"
    24    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    25    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    26    "/home/emsley/data/greg-data/alt-conf-waters.pdb"
    27    "/home/emsley/data/greg-data/backrub-fragment.pdb"
    28    "Copy_of_/home/emsley/data/greg-data/backrub-fragment.pdb"
    29    "/home/emsley/data/greg-data/coords-B3A.pdb"
    30    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT"
    31    "/home/emsley/data/greg-data/test-TER-OXT.pdb"
    32    "/home/emsley/data/greg-data/val.pdb"
    33    "/home/emsley/data/greg-data/2yie-frag.pdb"
    34    "/home/emsley/data/greg-data/4f8g.pdb"
    35    "/home/emsley/data/greg-data/4f8g.pdb"
    36    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    37    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    38    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    39    "Generic Masked Map"
    40    "difference-map"
    41    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    42    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    43    "averaged-map"
    44    "difference-map"
    45    "/home/emsley/data/greg-data/multi-carbo-coot-2.pdb"
    46    "/home/emsley/data/greg-data/monomer-VAL.pdb"
    47    "/home/emsley/data/greg-data/3ins-6B-3.0-no-peptide-D.pdb"
    48    "atom selection from tutorial-modern.pdb"
    49    "/home/emsley/data/greg-data/monomer-ACT.pdb"
    50    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    51    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    52    "atom selection from tutorial-modern.pdb"
    53    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    54    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    55    "/home/emsley/data/greg-data/rnase-A-needs-an-insertion.pdb"
    56    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    57    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    58    "/home/emsley/data/greg-data/pdb3hfl.ent"
    59    "/home/emsley/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT"
    60    "Ideal-A-form-RNA"
    61    "Ideal-A-form-RNA"
    62    "Ideal-A-form-DNA"
    63    "Ideal-A-form-DNA"
    64    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    65    "/home/emsley/data/greg-data/some-waters-with-ter.pdb"
    66    "/home/emsley/data/greg-data/tm+some-waters.pdb"
    67    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    68    "/home/emsley/data/greg-data/water-test-no-cell.pdb"
    69    "/home/emsley/data/greg-data/pathological-water-test.pdb"
    70    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    71    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    72    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    73    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    74    "/home/emsley/data/greg-data/pdb1hvv.ent"
    75    "/home/emsley/data/greg-data/monomer-ACT.pdb"
    76    "/home/emsley/data/greg-data/monomer-NPO.pdb"
    77    "SymOp_-X,-X+Y,-Z+1/3_Copy_of_74"
    78    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    79    "Copy_of_/home/emsley/data/greg-data/tutorial-modern.pdb"
    80    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    81    "/home/emsley/data/greg-data/pdb1py3.ent"
    82    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    83    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    84    "/home/emsley/data/greg-data/2goz-manip.pdb"
    85    "/home/emsley/data/greg-data/HOF.RES"
    86    "/home/emsley/data/greg-data/hollander.ins"
    89    "/home/emsley/data/greg-data/insulin.fcf"
    90    "atom selection from insulin.res"
    91    "atom selection from insulin.res"
    93    "/home/emsley/data/greg-data/horma-p21.res"
    94    "new-horma.ins"
    95    "/home/emsley/data/greg-data/crash.hat"
Reading coordinate file: /home/emsley/data/greg-data/2qd9.pdb
 PDB file /home/emsley/data/greg-data/2qd9.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 136 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "LGF"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LGF.cif
Reading coordinate file: /home/emsley/data/greg-data/2gtn.pdb
 PDB file /home/emsley/data/greg-data/2gtn.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 0/337
Molecule 137 read successfully
DEBUG:: there were 1 types with no dictionary 
INFO:: using standard CCP4 Refmac dictionary to search for "LIE"
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LIE.cif
INFO:: reference 136 has 169 atoms selected
INFO:: moving    137 has 169 atoms selected
superposing...
number of Ca atoms in selections: 21 (moving) and 21 (reference)
Another Go...

      Moving  Reference   Distance
      A 140 <---> A 140  : 0.180421   A
      A 141 <---> A 141  : 0.0760176   A
      A 142 <---> A 142  : 0.105242   A
      A 143 <---> A 143  : 0.124554   A
      A 144 <---> A 144  : 0.136965   A
      A 145 <---> A 145  : 0.138022   A
      A 146 <---> A 146  : 0.166154   A
      A 147 <---> A 147  : 0.274391   A
      A 148 <---> A 148  : 0.272752   A
      A 149 <---> A 149  : 0.117299   A
      A 150 <---> A 150  : 0.168421   A
      A 151 <---> A 151  : 0.0928138   A
      A 152 <---> A 152  : 0.120023   A
      A 153 <---> A 153  : 0.128061   A
      A 154 <---> A 154  : 0.253908   A
      A 155 <---> A 155  : 0.635071   A
      A 156 <---> A 156  : 0.130036   A
      A 157 <---> A 157  : 0.147806   A
      A 158 <---> A 158  : 0.223824   A
      A 159 <---> A 159  : 0.227128   A
      A 160 <---> A 160  : 0.23718   A

 Moving: YIHSADIIHRDLKPSNLAVNE
 Target: YIHSADIIHRDLKPSNLAVNE

INFO:: backup file coot-backup/_home_emsley_data_greg-data_2gtn.pdb_Fri_Sep_13_04:45:11_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal 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)  116.804 -94.6984 1.24908
  Rotation - euler (alpha,beta,gamma) 175.02 1.11487 -175.583
  Translation - Angstroms             0.320703 0.659802 0.881869 
INFO: core rmsd achieved: 0.221041 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
      sequence identity:           100%
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 138 read successfully
valid_labels(/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz,FWT,PHWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/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:: 0.016 seconds for FFT
INFO:: 0.001 seconds for statistics
      Map mean: ........ 1.06932e-09
      Map sigma: ....... 0.311501
      Map maximum: ..... 2.97757
      Map minimum: ..... -0.875045
INFO:: 0.019 seconds for contour map
INFO:: 0.062 seconds in total
INFO:: NCS chain comparison 93/93
First atom of 720 in first  selection 1/A/1 {ASP}/ N   altLoc :: segid :: pos: (44.878,12.955,8.761) 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)
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
INFO:: installing ghost map with name :Map 3 NCS found from matching Chain B onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
|    0.9637,  -0.07462,   -0.2563|
|    0.2651,    0.3804,     0.886|
|    0.0314,   -0.9218,    0.3864|
(     38.09,    -17.87,     14.32)
inverse of reference matcher transformation:
|    0.9637,    0.2651,    0.0314|
|  -0.07462,    0.3804,   -0.9218|
|   -0.2563,     0.886,    0.3864|
(    -32.42,     22.84,     20.06)
boxing over uvw = (  -0.04469,   -0.1739,   -0.2816) to uvw = (     1.228,    0.3332,    0.7985)
INFO:: There were 2 maps contributing to the average
INFO:: rescaling by 0.5
INFO:: 737280 out of 737280 (100%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: 0.00029312 st.d: 0.325007
Map statistics: min: -1.48938, max: 2.40191
 -1.3921    10
-1.19753    23
-1.00297    78
-0.808402    1162
-0.613838    12942
-0.419273    80812
-0.224709    194625
-0.0301443    193759
 0.16442    117773
0.358985    67091
0.553549    36147
0.748113    18238
0.942678    8655
 1.13724    3780
 1.33181    1483
 1.52637    485
 1.72094    128
  1.9155    65
 2.11006    18
 2.30463    6
 2.49919    0
INFO:: installing ghost map with name :Map 139 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 maps contributing to the average
INFO:: rescaling by 0.5
INFO:: 228096 out of 228096 (100%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: 0.000355333 st.d: 0.323619
Map statistics: min: -1.44957, max: 2.34115
 -1.3548    4
-1.16527    12
-0.975731    37
-0.786195    453
-0.596659    4596
-0.407123    26403
-0.217587    59478
-0.0280513    58289
0.161485    36006
0.351021    20752
0.540556    11414
0.730092    5769
0.919628    2875
 1.10916    1265
  1.2987    484
 1.48824    176
 1.67777    54
 1.86731    20
 2.05684    7
 2.24638    2
 2.43592    0
no diffs
NCS target chain has 93 peers.
Reading coordinate file: /home/emsley/data/greg-data/tutorial-modern.pdb
 PDB file /home/emsley/data/greg-data/tutorial-modern.pdb has been read.
Spacegroup: P 21 21 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 93/93
  INFO:: fill_ghost_info Constructed 1 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 144 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_0.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_2.pdb.gz
%%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe()
INFO:: NCS chain comparison 90/93
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 724 in second selection 1/B/4 {GLY}/ N   altLoc :: segid :: pos: (18.183,22.264,18.93) B-factor: 21.71
INFO:: LSQ matched 90 atoms
INFO:: 90 matched atoms had: 
   mean devi: 0.364276
    rms devi: 0.457135
    max devi: 2.1351
    min devi: 0.0880999
   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"
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_3.pdb.gz
INFO:: mutate 2 A to a TRP
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_4.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_tutorial-modern.pdb_Fri_Sep_13_04:45:14_2013_modification_5.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/pdb1t6q.ent
 PDB file /home/emsley/data/greg-data/pdb1t6q.ent has been read.
Spacegroup: C 2 2 21
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 110/110
INFO:: NCS chain comparison 110/110
  INFO:: fill_ghost_info Constructed 2 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
Molecule 145 read successfully
DEBUG:: there were 0 types with no dictionary 
INFO:: mutate 50 A to a ASP
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Fri_Sep_13_04:45:15_2013_modification_0.pdb.gz
%%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe()
INFO:: NCS chain comparison 109/110
First atom of 881 in first  selection 1/A/7 {GLY}/ N   altLoc :: segid :: pos: (31.795,49.973,50.866) B-factor: 68.18
First atom of 893 in second selection 1/B/6 {CYS}/ N   altLoc :: segid :: pos: (45.362,34.24,30.671) B-factor: 84.36
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had: 
   mean devi: 0.20482
    rms devi: 0.265098
    max devi: 1.17072
    min devi: 0.0159991
   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: (31.795,49.973,50.866) B-factor: 68.18
First atom of 881 in second selection 1/C/7 {GLY}/ N   altLoc :: segid :: pos: (47.664,58.992,25.996) B-factor: 67.72
INFO:: LSQ matched 110 atoms
INFO:: 110 matched atoms had: 
   mean devi: 0.227456
    rms devi: 0.303489
    max devi: 1.65495
    min devi: 0.0660944
   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:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Fri_Sep_13_04:45:15_2013_modification_1.pdb.gz
INFO:: backup file coot-backup/_home_emsley_data_greg-data_pdb1t6q.ent_Fri_Sep_13_04:45:15_2013_modification_2.pdb.gz
Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent
 PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 146 read successfully
DEBUG:: there were 0 types with no dictionary 
DEBUG ncs_control_change_ncs_master_to_chain_id imol: 146 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: (0.57,-74.72,-82.848) B-factor: 88.52
First atom of 540 in second selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.49888
    rms devi: 2.79624
    max devi: 6.68599
    min devi: 0.440067
   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: (0.57,-74.72,-82.848) B-factor: 88.52
First atom of 535 in second selection 1/C/190 {GLN}/ N   altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.6728
    rms devi: 2.9369
    max devi: 6.12
    min devi: 0.248273
   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: (0.57,-74.72,-82.848) B-factor: 88.52
First atom of 497 in second selection 1/D/193 {SER}/ N   altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had: 
   mean devi: 1.73174
    rms devi: 1.9769
    max devi: 7.94534
    min devi: 0.52974
   find_ncs_matrix returns (LSQ) 
|   -0.3815,   -0.9208,  -0.08098|
|   -0.9191,    0.3685,    0.1396|
|  -0.09874,    0.1277,   -0.9869|
(    -11.18,     4.757,    -127.2)
   Adding ghost with name: NCS found from matching Chain D onto Chain B
INFO:: NCS chain comparison 0/62
INFO:: set_ncs_master_chain Constructed 3 ghosts
   Ghost info:: NCS found from matching Chain A onto Chain B
   Ghost info:: NCS found from matching Chain C onto Chain B
   Ghost info:: NCS found from matching Chain D onto Chain B
Symmetry available for this molecule
INFO:: Matching/moving molecule number 147 to 146
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had: 
   mean devi: 0.223919
    rms devi: 0.23495
    max devi: 0.3369
    min devi: 0.0588188
INFO:: Axis orientation: (    0.7368,    0.6481,    0.1925)
INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426)
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:45:18_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal 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)
Symmetry available for this molecule
INFO:: Matching/moving molecule number 148 to 146
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had: 
   mean devi: 0.194298
    rms devi: 0.211186
    max devi: 0.358313
    min devi: 0.0328719
INFO:: Axis orientation: (    -0.431,    0.3986,    0.8095)
INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905)
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:45:18_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|   -0.6203,   -0.2279,   -0.7505|
|   -0.4559,   -0.6739,    0.5814|
|   -0.6382,    0.7028,    0.3141|
(    -22.14,    -19.93,     1.626)
INFO:: fractional coordinates matrix:
|   -0.8835,  -0.09252,    -0.543|
|   -0.5264,   -0.4107,    0.8789|
|   -0.4875,    0.7087,    0.3141|
(    -0.381,   -0.2605,   0.01406)
Symmetry available for this molecule
INFO:: Matching/moving molecule number 149 to 146
INFO:: LSQ matched 44 atoms
INFO:: 44 matched atoms had: 
   mean devi: 0.417399
    rms devi: 0.453088
    max devi: 0.792632
    min devi: 0.0759332
INFO:: Axis orientation: (    0.6231,   -0.7786,  -0.07411)
INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232)
INFO:: backup file coot-backup/Copy_of__home_emsley_data_greg-data_pdb1hvv.ent_Fri_Sep_13_04:45:18_2013_modification_0.pdb.gz
INFO:: coordinates transformed by orthonal matrix: 
|   -0.2227,   -0.9733,  -0.05471|
|   -0.9662,    0.2129,    0.1454|
|   -0.1299,   0.08525,   -0.9879|
(    -15.82,   -0.3228,      -130)
INFO:: fractional coordinates matrix:
|   -0.7806,   -0.3462,   0.03831|
|    -1.116,    0.7707,    0.2198|
|  -0.09924,     0.106,   -0.9879|
(   -0.1813,  -0.00422,    -1.125)
Reading coordinate file: /home/emsley/data/greg-data/pdb1hvv.ent
 PDB file /home/emsley/data/greg-data/pdb1hvv.ent has been read.
Spacegroup: P 31 2 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 62/67
INFO:: NCS chain comparison 66/67
INFO:: NCS chain comparison 61/67
INFO:: NCS chain comparison 0/67
  INFO:: fill_ghost_info Constructed 3 ghosts
      Ghost 0 name: "NCS found from matching Chain B onto Chain A"
      Ghost 1 name: "NCS found from matching Chain C onto Chain A"
      Ghost 2 name: "NCS found from matching Chain D onto Chain A"
Molecule 150 read successfully
DEBUG:: there were 0 types with no dictionary 
valid_labels(/home/emsley/data/greg-data/1hvv_sigmaa.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1
INFO:: making map from mtz filename /home/emsley/data/greg-data/1hvv_sigmaa.mtz
Number of OBSERVED reflections: 20903
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 112, 112, 150)
INFO:: 0.039 seconds to read MTZ file
INFO:: 0.023 seconds to initialize map
INFO:: 0.026 seconds for FFT
INFO:: 0.002 seconds for statistics
      Map mean: ........ -1.58391e-06
      Map sigma: ....... 0.224074
      Map maximum: ..... 1.72187
      Map minimum: ..... -0.881789
INFO:: 0.009 seconds for contour map
INFO:: 0.099 seconds in total
INFO:: NCS chain comparison 62/67
First atom of 540 in first  selection 1/A/190 {GLN}/ N   altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26
First atom of 506 in second selection 1/B/193 {SER}/ N   altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52
INFO:: LSQ matched 62 atoms
INFO:: 62 matched atoms had: 
   mean devi: 2.49888
    rms devi: 2.79624
    max devi: 6.68599
    min devi: 0.440067
   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: (-13.535,-64.438,-56.928) B-factor: 45.26
First atom of 535 in second selection 1/C/190 {GLN}/ N   altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76
INFO:: LSQ matched 66 atoms
INFO:: 66 matched atoms had: 
   mean devi: 1.97132
    rms devi: 2.1729
    max devi: 4.54109
    min devi: 0.429522
   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: (-13.535,-64.438,-56.928) B-factor: 45.26
First atom of 497 in second selection 1/D/193 {SER}/ N   altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35
INFO:: LSQ matched 61 atoms
INFO:: 61 matched atoms had: 
   mean devi: 3.70416
    rms devi: 4.0859
    max devi: 9.43828
    min devi: 0.285802
   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 151 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 151 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 151 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 maps contributing to the average
INFO:: rescaling by 0.25
INFO:: 313712 out of 313712 (100%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: -0.000831257 st.d: 0.176659
Map statistics: min: -0.997714, max: 1.48656
-0.935607    4
-0.811393    18
-0.687179    139
-0.562965    686
-0.438751    3580
-0.314537    13684
-0.190323    43824
-0.0661091    105065
0.0581048    85978
0.182319    35332
0.306533    15214
0.430747    6068
0.554961    2422
0.679174    947
0.803388    405
0.927602    206
 1.05182    85
 1.17603    38
 1.30024    9
 1.42446    8
 1.54867    0
INFO:: installing ghost map with name :Map 151 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 151 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 151 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 maps contributing to the average
INFO:: rescaling by 0.25
INFO:: 313712 out of 313712 (100%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: -0.000831257 st.d: 0.176659
Map statistics: min: -0.997714, max: 1.48656
-0.935607    4
-0.811393    18
-0.687179    139
-0.562965    686
-0.438751    3580
-0.314537    13684
-0.190323    43824
-0.0661091    105065
0.0581048    85978
0.182319    35332
0.306533    15214
0.430747    6068
0.554961    2422
0.679174    947
0.803388    405
0.927602    206
 1.05182    85
 1.17603    38
 1.30024    9
 1.42446    8
 1.54867    0
INFO:: installing ghost map with name :Map 151 NCS found from matching Chain B onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 151 NCS found from matching Chain C onto Chain A
Done install_ghost_map
INFO:: installing ghost map with name :Map 151 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 maps contributing to the average
INFO:: rescaling by 0.25
INFO:: 313712 out of 313712 (100%) map points  were masked out of NCS average target volume,  chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: -0.000831257 st.d: 0.176659
Map statistics: min: -0.997714, max: 1.48656
-0.935607    4
-0.811393    18
-0.687179    139
-0.562965    686
-0.438751    3580
-0.314537    13684
-0.190323    43824
-0.0661091    105065
0.0581048    85978
0.182319    35332
0.306533    15214
0.430747    6068
0.554961    2422
0.679174    947
0.803388    405
0.927602    206
 1.05182    85
 1.17603    38
 1.30024    9
 1.42446    8
 1.54867    0
error (syntax error)
error (syntax error)
error (not syntax error)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
NameError: name 'rr_not_found_thing' is not defined
Reading coordinate file: /home/emsley/data/greg-data/monomer-ACT.pdb
 PDB file /home/emsley/data/greg-data/monomer-ACT.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
Molecule 160 read successfully
DEBUG:: there were 0 types with no dictionary 
Entering test: OXT in restraints?
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/
There are 125 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif
There are 1 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif
There are 2 data in /home/emsley/data/greg-data/libcheck_BCS.cif
PASS: OXT in restraints?
Entering test: Relative file name
PASS: Relative file name
Entering test: geometry distortion comparision
    Good gdi < exception thrown
    Good gdi > exception thrown
PASS: geometry distortion comparision
Entering test: test symm trans to origin
    Got length 0.141421
PASS: test symm trans to origin
Entering test: test lsq plane
LSQ deviations: 0 1.22483e-17
PASS: test lsq plane
Entering test: test COO modification
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/
There are 125 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ALA.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASP.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ASN.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLN.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLY.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GLU.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PHE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HIS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/i/ILE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LYS.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/l/LEU.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MET.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/m/MSE.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PRO.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/ARG.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SER.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/THR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/v/VAL.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TRP.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/t/TYR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/p/PO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/s/SO4.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GOL.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CIT.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/AR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CR.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/CD.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/GD.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/a/A.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/c/C.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/g/G.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/u/U.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/d/DT.cif
There are 2 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/h/HOH.cif
There are 1 data in /home/emsley/ccp4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif
Reading coordinate file: /home/emsley/data/greg-data/hideous-OXT.pdb
 PDB file /home/emsley/data/greg-data/hideous-OXT.pdb has been read.
Spacegroup: P 21 21 21
read 9 atom 
created 7 bond       restraints 
created 8 angle      restraints 
created 1 plane      restraints 
created 1 chiral vol restraints 
created 2 torsion restraints 
created 23 restraints

INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 93 and 93 of chain A
Link restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints)
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints)
Flanking residue restraints: 
   0 bond    links
   0 angle   links
   0 plane   links
initial distortion_score: 10113.4
    Initial RMS Z values
bonds:      3.72079
angles:     7.46884
torsions:   0.276426
planes:     16.9011
non-bonded: 221.797
chiral vol: 1.22665
rama plot:  N/A 
start_pos:  N/A 
Minimum found (iteration number 946) at 24.2085
    Final Estimated RMS Z Scores:
bonds:      1.14991
angles:     1.01461
torsions:   0.0248459
planes:     0.00133524
non-bonded: 0.0833607
chiral vol: 0.00317726
rama plot:  N/A 
start_pos:  N/A 
refinement_took 0.022 seconds
OXT out of plane distance: 7.81835e-05
OXT->O distance: 2.27418
PASS: test COO modification
Entering test: remove whitespace
PASS: remove whitespace
Entering test: Residues for phi,psi are close enough to be considered linked
Reading coordinate file: /home/emsley/data/greg-data/frag-2wot.pdb
 PDB file /home/emsley/data/greg-data/frag-2wot.pdb has been read.
Spacegroup: P 21 21 21
bad residues for phi,psi calculation
bad residues for phi,psi calculation
PASS: Residues for phi,psi are close enough to be considered linked
    96    "coot-ccp4/monomer-3GP.pdb"
    97    "/home/emsley/data/greg-data/monomer-3GP.pdb"
    98    "/home/emsley/data/greg-data/test-LIG.pdb"
    99    "/home/emsley/data/greg-data/test-LIG.pdb"
    100    "/home/emsley/data/greg-data/monomer-NPO.pdb"
    101    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    102    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    103    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    104    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    105    "Copy_of_/home/emsley/data/greg-data/monomer-NPO.pdb"
    106    "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb"
    107    "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT"
    108    "/home/emsley/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT"
    109    "Masked (by protein)"
    110    "Fitted ligand #0-0"
    111    "Fitted ligand #0-1"
    112    "Fitted ligand #1-0"
    113    "Fitted ligand #1-1"
    114    "Fitted ligand #2-0"
    115    "Fitted ligand #2-1"
    116    "Fitted ligand #2-2"
    117    "Fitted ligand #3-0"
    118    "Fitted ligand #4-0"
    119    "Fitted ligand #5-0"
    120    "Fitted ligand #6-0"
    121    "Fitted ligand #7-0"
    122    "Fitted ligand #8-0"
    123    "Fitted ligand #9-0"
    124    "Fitted ligand #9-1"
    125    "coot-ccp4/monomer-3GP.pdb"
    126    "Copy_of_coot-ccp4/monomer-3GP.pdb"
    127    "/home/emsley/data/greg-data/dipole-residues.pdb"
    128    "/home/emsley/data/greg-data/tutorial-modern.pdb"
    129    "/home/emsley/data/greg-data/crashes_on_cootaneering-v2.pdb"
    130    "/home/emsley/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT"
    131    "Ideal-A-form-RNA"
    134    "/home/emsley/data/greg-data/1wly.pdb"
    135    "/home/emsley/data/greg-data/1yb5.pdb"
PASS: SSM - Alice Dawson's Example
Entered testcase - SSM by atom selection [JED Example]
PASS: SSM by atom selection [JED Example]
Ended 06-ssm.scm
Running 07-ncs.scm ...
Entered testcase - NCS maps test
PASS: NCS maps test
Entered testcase - NCS chains info
   NCS info: (("A" "B"))
PASS: NCS chains info
Entered testcase - NCS deviation info
PASS: NCS deviation info
Entered testcase - NCS Residue Range copy
PASS: NCS Residue Range copy
Entered testcase - NCS Residue Range edit to all chains
result: (#t #t)
PASS: NCS Residue Range edit to all chains
Entered testcase - Manual NCS ghosts generates correct NCS chain ids
   NCS ghost chain IDs pre:  (("B" "A" "C" "D"))
   NCS ghost chain IDs post: (("B" "A" "C" "D"))
PASS: Manual NCS ghosts generates correct NCS chain ids
Entered testcase - NCS maps overwrite existing maps
==== test-name: "Map 151 NCS found from matching Chain B onto Chain A"   n-matchers: 2
==== test-name: "Map 151 NCS found from matching Chain C onto Chain A"   n-matchers: 2
==== test-name: "Map 151 NCS found from matching Chain D onto Chain A"   n-matchers: 2
PASS: NCS maps overwrite existing maps
Ended 07-ncs.scm
Running 08-utils.scm ...
Entered testcase - Test key symbols
WARNING:: could not find key-sym-code for "missing key"
PASS: Test key symbols
Entered testcase - Test running a Python function
   test_val_2 passed
   test_val_3 passed
PASS: Test running a Python function
Entered testcase - Internal/External Molecule Numbers match
PASS: Internal/External Molecule Numbers match
Entered testcase - spacegroup operators to space group conversion
PASS: spacegroup operators to space group conversion
Ended 08-utils.scm
Running 09-internal.scm ...
Entered testcase - Test internal functions
PASS: Test internal functions
Ended 09-internal.scm

                === greg-tests Summary ===

# of testcases attempted   114
# of expected passes       114
# of expected failures     0
# of unexpected passes     0
# of unexpected failures   0
# of unresolved testcases  0
# of unsupported testcases 0
# of untested testcases    0


                === Summary of all tests ===

# of tools                 1
# of testcases attempted   114
# of expected passes       114
# of expected failures     0
# of unexpected passes     0
# of unexpected failures   0
# of unresolved testcases  0
# of unsupported testcases 0
# of untested testcases    0
# of files abandoned       0


Some deprecated features have been used.  Set the environment
variable GUILE_WARN_DEPRECATED to "detailed" and rerun the
program to get more information.  Set it to "no" to suppress
this message.
test_coot: coot test passed